Neuroinformatics Working Group

Update10/26/2009

H Jeremy Bockholt

Multi-Site User Query

Results with standard descriptions in HID (i.e. data provenance)

Result Images and XML wrapper in Data Grid

FIPS Results

FIPS: FSL Image Processing Scripts

HID(s)(Local)

Data Grid(Local)

fMRI Scanner

Clinical Data•Computer aided scale input via clinical data entry interface

FBIRN WorkflowFBIRN Workflow

DICOM, NIFTIDICOM, NIFTI

FMRI Images•Automated image upload to Data Grid/HID for sharing

Upload Script Updates

Upload Script/GUI Updates

Support for non-DICOM files Supports custom rule definitions File sorting and reorganization

Sample dataset Improved installation Improved documentation Sub-group permissions Bug fixes Full NITRC hosting Readiness for humanQA and phaseIII I/P

Multi-Site User Query

Results with standard descriptions in HID (i.e. data provenance)

Result Images and XML wrapper in Data Grid

FIPS Results

FIPS: FSL Image Processing Scripts

HID(s)(Local)

Data Grid(Local)

fMRI Scanner

Clinical Data•Computer aided scale input via clinical data entry interface

FBIRN WorkflowFBIRN Workflow

DICOM, NIFTIDICOM, NIFTI

FMRI Images•Automated image upload to Data Grid/HID for sharing

Clinical Tablet PC

Assessment design for Jansen study and PhaseIII

Interface testing – clinicians Improved user interface

Tablet fully tested with postgreSQL HID Tested remote HID data import via webservices All but one site Tablets configured/delivered

(UCSD I/P) Updated software Bug fixes Full NITRC hosting

Multi-Site User Query

Results with standard descriptions in HID (i.e. data provenance)

Result Images and XML wrapper in Data Grid

FIPS Results

FIPS: FSL Image Processing Scripts

Data Grid(Local)

fMRI Scanner

Clinical Data•Computer aided scale input via clinical data entry interface

FBIRN WorkflowFBIRN Workflow

DICOM, NIFTIDICOM, NIFTI

FMRI Images•Automated image upload to Data Grid/HID for sharing

HID

HID Updates

CVS release Oracle – PostgreSQL migration scripts Improved upgrade instructions All sites migrated, MGH (in last phase of migration) Upgraded support for GridFTP and RLS services (in

progress) Webservice support for tablet PC Webservice support for XCEDE derived data Upgraded support for user management given new

security infrastructure (DONE) Added CMINDs neurocognitive battery data import

~14 new assessments Full NITRC hosting

Multi-Site User Query

Results with standard descriptions in HID (i.e. data provenance)

Result Images and XML wrapper in Data Grid

FIPS Results

FIPS: FSL Image Processing Scripts

fMRI Scanner

Clinical Data•Computer aided scale input via clinical data entry interface

FBIRN WorkflowFBIRN Workflow

DICOM, NIFTIDICOM, NIFTI

FMRI Images•Automated image upload to Data Grid/HID for sharing

HID

Data Grid

SRB – GridFTP Migration

Sites downloaded FBIRN collected data and local user data off SRB

Worked with BIRN-CC to set up cron jobs that automatically download new BIRN users and groups as the are added

Tested RLS location service User management Full Replication (Iowa and UCI have full copy of

all data) I/P

Multi-Site User Query

HID(s)(Local)

Data Grid(Local)

fMRI Scanner

Clinical Data•Computer aided scale input via clinical data entry interface

FBIRN WorkflowFBIRN Workflow

DICOM, NIFTIDICOM, NIFTI

FMRI Images•Automated image upload to Data Grid/HID for sharing

Results with standard descriptions in HID (i.e. data provenance)

Result Images and XML wrapper in Data Grid

FIPS Results

FIPS: FSL Image Processing Scripts

Derived Data Management

Added pipeline provenance tables to HID schema Webservices for importing XCEDE formatted

derived data/metadata Build query interface for derived data

Tested on phase II structural study Tested Pre-Processing pipeline provenance in

XCEDE and HID Deployment of HID related changes in latest

PostgreSQL release Transition work has slowed progress of derived

data management, down, hopefully we can return to this soon.

Slicer3 Developments - FBIRN

Slicer3-related efforts for fBIRN:

User-centered Slicer3 design & implementation

FIPS2MRML conversion tool

XCEDE catalog and XNAT Enterprise catalog support

Slicer3’s QueryAtlas release

Remote I/O infrastructure

FetchMI informatics tool for REST-based web services

QueryAtlas for fBIRN & mBIRN

Cross-Testbed Activity

Compatible with fMRI and Morphometry Datasets in

BIRN-Standard Formats

Provides a Link Between Images and Publication

Databases

Uses Anatomic Labeling + Ontologies

Links to Definitions, Publications, Quantifications

e.g. Wikipedia, PubMed, IBVD, BrainInfo

Transition Tasks

Hardware reconfiguration for local site administration (all sites done at this point)

Downloading all data off SRB (done) SRB out, GridFTP in

Is there life after SRB? (somewhat) Will GridFTP save us time?

What is time? Who are “us”?

Updating of tools for GridFTP / authentication Testing all tools in coordination with new

infrastructure

Multi-Site User Query

HID(s)(Local)

GridFTP

fMRI Scanner

Clinical Data•Computer aided scale input via clinical data entry interface

““New” FBIRN WorkflowNew” FBIRN Workflow

DICOM, NIFTIDICOM, NIFTI

FMRI Images•Automated image upload to Data Grid/HID for sharing

Results with standard descriptions in HID (i.e. data provenance)

Result Images and XML wrapper in Data Grid

FIPS Results

FIPS: FSL Image Processing Scripts

RLS

‘09 AHM Discussion Topics

Tu:8:30-9:00am - Review grant milestones 9:00 – 9:45am - Janssen + Phase III data collection, uploads, tablet assessments, CMINDs data discussion 9:45 – 10:00am - Permissions auditing for data uploads10:15 – 10:45am - Derived data: identify datasets, work, timelines10:45 – 12:00pm - GridFTP – infrastructure issues discussion with BIRN-CC about working strategies to test fixes and address issues, no solutions currently:

BIRNDATA-54: Reliability of GridFTP transfers - This is the reliability issue that Dingying reported recently to the ops-wg listBIRNDATA-55: Performance of GridFTP transfers - This is the performance issue that Syam reported a while ago to the ops-wg listBIRNDATA-56: GridFTP permissions - This is the extended ACL proposal that Syam reported to the ops-wg list and documented on the xwikiBIRNDATA-57: Remote synchronization of GridFTP directories - This is the request for rsync-like functionality that Jessica and others have reported to the ops-wg list in the past