Post on 17-Jan-2016
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