A Grid Approach to Distributed Image Analysis for Early Diagnosis of Alzheimer Disease Roberto Barbera (a nome di Livia Torterolo) Università di Catania e INFN Primo Workshop TriGrid VL Catania, 13.03.2006

Agenda Introduction to SPM analysis and to development of a web-based SPM service GRID implementation of SPM service Current Status and Plans Catania, Primo Workshop TriGrid VL, 13.03.2006

Partners The first part of the work has been done during the Italian Neuroinformatics OCSE Node project in collaboration with San Raffaele Hospital of Milano University of Milano – Bicocca GRID implementation has been carried out by Bio-Lab at DIST, University of Genoa, during the Grid.it Italian project The application is a quite stable work in progress and served as a demostrator for the Grid.it project but further developments and extensions are in progress still inside the GILDA testbed Catania, Primo Workshop TriGrid VL, 13.03.2006

Introduction to Alzheimer Disease AD is the most common form of dementia, accounting from 50% to 70% of all dementias in elderly people (around 3 million people in EU25) Clinically, AD is characterized by a progressive loss of cognitive abilities Memory loss is typically the earliest sign of AD Catania, Primo Workshop TriGrid VL, 13.03.2006

Analysis of PET-SPECT images Catania, Primo Workshop TriGrid VL, 13.03.2006

SPM Results Results of a SPM analysis on a PET study of glucose metabolism in a patient with dementia. Ipometabolic pattern in the frontal cortex: design matrix (top right), statistically significant clusters on a glass brain in three orthogonal planes (top left) and on a 3D brain rendering (bottom) Catania, Primo Workshop TriGrid VL, 13.03.2006

Why a portal? http://www.neuroinf.it The remote access to SPM analysis could provide doctors from peripheral hospitals with an invaluable tool to run the analysis remotely only using a standard browser web No particular HW resources or computer knowledge are required In order to avoid errors during the analysis, only selected users should access and use the service http://www.neuroinf.it http://www.neuroinf.it Catania, Primo Workshop TriGrid VL, 13.03.2006

SPM: Why GRID? A large set of images of normal patients is required to be used for comparison PET and SPECT studies on normal subjects are very rare Images of patients are covered by privacy and security issues and for this reason they cannot be freely moved on the net or published by the centre that made the analysis Catania, Primo Workshop TriGrid VL, 13.03.2006

Contribution to GILDA LCG Grid Environment v. 2.6.0. 6 machines dedicated to LCG NODE: 1 CE, 1 SE, 3 WNs, 1 UI, 1 LCG install server (12 CPUs, 7Giga (RAM), ≈ 350Giga of storage) Catania, Primo Workshop TriGrid VL, 13.03.2006

LCG tools used Data Management and File Access tools: to access data from User Interface using Logical File Names (LFN) LCG File Catalog (LFC): to register data into the catalog AMGA Metadata Catalog: to add related metadata to data Catania, Primo Workshop TriGrid VL, 13.03.2006

Data Management and File Access Catania, Primo Workshop TriGrid VL, 13.03.2006

GRID-Design of the application With reference to different LCG tools mentioned above, application code has been modified in the following way: Registration and storage of data files (PET/SPECT images) on SEs available using lcg_utils interacting with LFC and AMGA. Development of a C program with GFAL C API in order to access distributed images using their LFNs and to extract some information necessary to SPM analysis without copying them locally. Job Submission: creation of a JDL file to submit the executable (and not the images) with GFAL call to the GRID. Statistical Analysis: running of SPM analysis from results obtained from job submission. Statistical analysis is performed outside GRID environment. Catania, Primo Workshop TriGrid VL, 13.03.2006

Final GRID structure Catania, Primo Workshop TriGrid VL, 13.03.2006

Application Running: Setting Parameters Setting SPM parameters Selection of normal subjects QUERIES to AMGA ! Catania, Primo Workshop TriGrid VL, 13.03.2006

Application running: JOB SUBMISSION SPM Analysis RESULTS Catania, Primo Workshop TriGrid VL, 13.03.2006

Current Status and Plans Application pre-processing parallelization (further functions to port on Grid) Interface move to Genius 3.1 Overall framework improve performance and scalability A Grid environment devoted to the analysis of microarrays, derived from this project, will be tested  in the frame of European Project BioinfoGRID http://www.itb.cnr.it/bioinfogrid (Bioinformatics Application for Life Science) A bioinformatics data storage and analysis platform with metadata support will be developed under Italian MIUR-FIRB project LITBIO www.litbio.org (Laboratory for Interdisciplinary Technologies in Bioinformatics) Thanks for your attention! Catania, Primo Workshop TriGrid VL, 13.03.2006