Neuroinformatics Working Group Update 10/26/2009 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 Workflow DICOM, 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 Workflow DICOM, 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 Workflow DICOM, 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 Workflow DICOM, 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 Workflow DICOM, 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 Workflow DICOM, 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 uploads 10:15 – 10:45am - Derived data: identify datasets, work, timelines 10:45 – 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 list BIRNDATA-55: Performance of GridFTP transfers - This is the performance issue that Syam reported a while ago to the ops-wg list BIRNDATA-56: GridFTP permissions - This is the extended ACL proposal that Syam reported to the ops-wg list and documented on the xwiki BIRNDATA-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