CCB Special Interest Group on Automated Pipeline Workflows for Neuroimaging Data Analysis

Overview

The SIG-FLOW group meets regularly to address challenges and report progress on the Design, Revisions, Validation and Dissemination of old and new Pipeline workflows.

Members

• AlenZamanyan
• ShruthiChakrapani
• IvoDinov
• Other Pipeline Developers

Meeting Data/Time/Place

• The SIG-FLOW group meeting is meeting Tue/Thu, 11:00AM in T-Room

Currently Discussed Pipeline Workflows

• Minimum Distance Template (MDT), Atlasing
• Tensor Based Morphometry (TBM), Cal Tech
• Stats Tools Modules
• Datasets and Atlases
• Auto Tissue Volume Workflow (auto calculation of total WM GM ICV volumes)
• Global Shape Analysis (GSA)
• ShapeTools^? Modules/Pipelines
• fMRI/FEAT
• Local Shape Analysis (LSA)
• Automated 56 ROI volume extraction workflow
• Direct Hippo Mapping (DHM, Yonggang) workflow
• Others

Progress & Status

• 11/24/09
• 11/19/09
• 11/17/09
• 11/12/09
• 11/10/09
• 11/05/09
• 11/03/09
• 10/29/09
• 10/27/09
• 10/22/09
• 10/20/09
• 10/15/09
• 10/13/09
• 10/06/09
• 10/01/09
• 09/29/09
• 09/24/09
• 09/22/09
• 09/17/09
• 09/15/09
• 09/10/09
• 08/27/09
• 08/25/09
• 08/20/09
• 08/18/09
• 08/11/09
• 08/06/09
• 07/30/09
• 07/28/09
• 07/23/09
• 07/21/09
• 07/16/09
• 07/14/09
• 07/09/09
• 07/07/09
• 06/30/09

Protocols for committing Pipeline Libraries and Workflows to production

The following 2 protocols should be followed to commit tools/libraries and pipeline workflows to production.

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.

LONI Grid Server Matrix

Hostname	Alias	CPU/Slot Count	Status	Ownership
pipeline‐lsh1.loni.ucla.edu	try-me	8	production	sysadmin & pipeline
cerebro‐lsh1.loni.ucla.edu	pipeline-dev	16	development	pipeline
cerebro‐lsh2.loni.ucla.edu	cranium primary	590	production	sysadmin & pipeline
cerebro‐lsh3.loni.ucla.edu	cranium secondary	590	production	sysadmin & pipeline
cerebro‐lsh5.loni.ucla.edu	pipeline-qa	192	development/qa	pipeline
cerebro‐lsh6.loni.ucla.edu	pipeline-ext	50	production	sysadmin & pipeline