View source for CTSC Brad Dickerson, MGH

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=Mission=
See http://www.nmr.mgh.harvard.edu/~bradd/research.html


=Use-Case Goals=
The first two steps in the retrospective OFRR1 (Object Free Recall and Recognition) use-case include Basic Data Management and Query Formulation. (Eventually want to upload two projects with matching subjectIDs).
* '''Step 1: Data Management'''  Describe and upload retrospective OFRR1 datasets (roughly 1 terabyte) and confirm appropriate organization and naming scheme via web GUI.
* '''Step 2: Query Formulation'''
** make specific queries using XNAT web services, 
** ensure that query results match those returned by analogous searches on the local file system.

=Participants=
* sites involved: MGH NMR center
* number of users: >10
* PI: Brad Dickerson
* staff: Akram Bakkour & Mike Brickhouse (Study coordinator/MRI technician/Lab manager) 
* clinicians
* IT staff: NMR could provide IT support

=Outcome Metrics=
'''Step 1: Data Management'''
* Visual confirmation (via web GUI) that all data is present, organized and named appropriately
* How quickly can data of interest be identified via web GUI
* Can data be successfully & efficiently downloaded from XNAT to local file system.
* How does network interruption affect query/download process.
* other?
'''Step 2: Query Formulation'''
*  Successful tests that responses to XNAT queries (for all subjectIDs within some age range and with an MR with particular resolution) results returned from search on the local file system.

=Fundamental Requirements=
* accessibility
* redundancy
* enough documentation to support novice users / developers: as Mike Brickhouse comes up to speed, he will provide feedback about what was missing or challenging in the existing XNAT documentation.

=Data=
The Dickerson lab has about 250 scans for their own studies, and 150 scans for collaborators. Scans include both MRI and fMRI. Other data are stored with Excel spreadsheets. 
**Project
**Imaging Modalities
**Genetic

For this OFRR1 use-case, approximately 80 sessions comprise the retrospective data. Data consists of
* MRI (DICOM, .mgz, NIFTI)
* Clinical and Behavioral data ascii text (.txt)
* fMRI paradigms (eprime)
* '''Some data may contain protected medical information'''

*Storage needs
Images files are currently distributed over several file servers on the same network.

=Workflows=
==Current Data Management Process==
DICOM files are transferred from the scanners (PACS?) to a local DICOM Server, and then copied to lab machines
Images are processed with FreeSurfer.

**Other software to be integrated (e.g., Osirix)
**other features

==Target Data Management Process (Step 1.)==

(schematic to come)

* Data from multiple file systems will be described and uploaded via an upload script or a light client into a single OFRR1 project on XNAT;

== Target Query Formulation (Step 2.)==
'''Step 2.''' Develop Query capabilities using scripted client calls to XNAT web services, such as:

 Show all subjectIDs with age > 60 & MR with resolution=0.38mm
 Show all subjectIDs with age < 20 & MR with resolution=0.38mm

* Useful product would be a list (csv file?) of appropriate subject IDs, or
* Useful product would be a list of URIs of appropriate datasets



=Other Information=

There have been at least two serious attempts using XNAT, working with XNAT support group (NRG) at Harvard. An XNAT with customized schema was developed by Eli White a couple of years ago on Dory at NMR.

The lab recognizes the need for an XNAT-based system to manage images and other data.