Workshop Attendees

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XNAT Presenters

  Name Brief Bio Talks Scheduled

Dan Marcus

Director

Dan directs the NRG. His informatics interests include data sharing, data mining, and high throughput processing.

His scientific interests include neural coding and connectivity, brain morphometry, automatic diagnostics, and genetics of cognitive and neurological phenotypes.

  • Day 1: Daily Welcome
  • Day 1: XNAT for Newbies
  • Day 2: Daily Welcome
  • Day 2: XNAT for Oncology (supplemental talk)
  • Day 3: Daily Welcome
  • Day 4: Daily Welcome
  • Day 5: Daily Welcome

Rick Herrick

Lead XNAT Developer

Raised in the Deep South (Tampa), Rick was moved to California by the U.S.A.F., where he adapted well to the mild weather.

He graduated from U.C. Santa Cruz (go Slugs, 1991 National Champion in Ultimate Frisbee!) with a degree in Politics. He met his future wife while attending Avocado Sundae shows. They got married, had a daughter, moved to Long Beach, CA, hated the L.A. traffic, and now reside in Webster Groves, MO.

Rick drives a Jeep Wrangler, plays guitar (Paul Reed Smith, Stratocaster, Yamaha acoustic) and mandolin (Flatiron A-style), has two dogs (Frankie, who’s a girl, and Shaggy, who’s not), a cat (Oliver), and favors the “ribs” food group.

Rick does Java and .NET, with a strong emphasis on internal plumbing.

  • Day 1: Install and Basic Use of XNAT
  • Day 1: Practical Session
  • Day 4: XNAT Under the Hood
  • Day 4: XNAT Customization
  • Day 4: Practical Session (Lead)

Jenny Gurney

CNDA Dev / Admin

Jenny joined the NRG in 2009 and currently oversees CNDA operations.

She completed her MS in Computer Science at Washington University and also has a somewhat disused BA in Spanish Literature from UNC-Chapel Hill (Go Heels!).

Jenny is a St. Louis native and enjoys spending time with her husband and two young boys, most of which is spent bouncing between the zoo, science center, and Museum of Transportation.

  • Day 1: XNAT Administration
  • Day 1: Practical Session
  • Day 2: XNAT At Scale

Chip Schweiss

IT Operations Lead

Chip joined NRG in 2010 as a systems engineer, and is now our IT Operations Lead.

His accomplishments include (but are not limited to) architecting and building our high-availability ZFS storage pool, Puppet-based XNAT virtual machine deployments, and drive duplication systems for the Human Connectome Project.

A native of the St Louis region (broadly defined), Chip also routinely wins our internal cake and pastry bake-offs.

  • Day 2: IT Planning
  • Day 2: XNAT At Scale
  • Day 2: Practical Session

Mohana Ramaratnam

XNAT Pipeline Developer

Mohana holds a Masters in Mathematics from University of Pune, India. She has developed XNAT’s image visualization and automated processing technologies since its inception. Mohana cooks a mean curried chicken and is a proud mother.
  • Day 3: Pipelines
  • Day 3: Practical Session
  • Day 4: XNAT to XNAT Data Synchronization (supplemental talk)

John Flavin

XNAT Pipeline Developer

Flavin (nobody ever calls him "John") does pipeline development for the CNDA, and development on Automation and Container Services for XNAT.

He graduated from WashU in 2012 with his PhD in Physics, and after spending a year working for a St. Louis tech startup, he found his way back to campus (albeit on the other side of Forest Park from where he began).

Flavin has BS degrees in Physics and Math from Mizzou. A St. Louis native currently residing in Webster Groves, he enjoys bicycling with his wife, Gayle, and their son.

  • Day 3: Automation
  • Day 3: Practical Session

Tim Olsen

XNAT Developer In Emeritus

Tim is the original lead developer of XNAT, which makes him the figurative grandfather of all XNAT code. Tim is also the literal father of five children who have come into the world since the inception of XNAT 1.0.

Tim currently lives in Bloomington IL and continues to develop code for the extended XNAT universe, including clinical trial applications of XNAT.

  • Day 1: XNAT for Clinical Trials (Supplemental Talk)
  • Day 4: XNAT Customization

Justin Cleveland

XNAT Developer

Justin joined the XNAT Team in 2013, and almost immediately plunged into the deep end of the Visits and Protocols development universe. Justin contributes in equal measures to front end and back end development, is an advocate of Angular development, and also has the somewhat thankless task of being our daily scrum master.

In his spare time, Justin spends a lot of time outdoors and has quite a few stories to tell from the Black Rock desert in Nevada, which he may or may not tell you.

  • Day 2: Visits and Protocols Plugin (Supplemental Talk)

Charlie Moore

XNAT Tester / Chaos Monkey

While working part time with the XNAT team, Charlie completed a Bachelor's degree at Washington University with majors in Mathematics and Economics. Now joining the lab full time, Charlie focuses on Chaos Monkey activities (breaking XNAT), and automated test development. Outside of the office, Charlie spends his time training for his backup career as a professional StarCraft 2 player, and tending to his ever-growing collection of plushies.

  • Day 2: Automated Test Suites for XNAT (Supplemental Talk)

Will Horton

UI / UX Designer

Will is our resident creative guy, carrying a Bachelor of Fine Arts degree from Washington University, and arrives on the team after running a freelance information design studio for eight years. He takes workflows, business rules, UX principles and cool interaction concepts seen on your favorite app du jour, and outputs new-fangled wireframes and designs for XNAT.

If you were to draw a Venn diagram of people who love football and bowling and people who love to draw Venn diagrams, Will would be one of the few in its slim center.

  • Day 3: XNAT Container UI Wireframes (Supplemental Talk)

Mike Hodge

XNAT Developer

Mike is a programmer who joins our group to work on the ConnectomeDB application for the Human Connectome project. He comes to us by way of a local health care system where he worked on support and development of a large clinical application and prior stints at the medical school developing study/data management applications.

He enjoys playing Wii with his sons, and when he can tear them away from that, enjoys trips to the City Museum, science center, zoo, Six Flags and discussions with them on their latest interests.

  • Day 5: Talks TBA

Mark Florida

Lead UI Developer

Mark joined the XNAT team in 2012, fell backwards out of his chair at the state of XNAT's UI code, got back into his chair and has been steadily working to improve it ever since.

Mark is a refugee from the world of free-lance corporate web design, and is happily ensconced as a full-time XNAT UI developer. He is bringing up his three children in the holy musical trinity of Nirvana, Black Flag and old-school hip hop. In his spare time he fiddles with photography, digital music, and early 80’s Toyota Celicas.

 

Misha Milchenko

Pipeline Developer

Misha focuses on mathematical and image processing aspects of programming tasks in the group. He is also interested in brain research from right-to-left hemisphere perspective.

He is a friend of Italian opera in ways permissible by local, state and federal laws, prefers moderate realism over radical cubism in fine arts, and languages obsolete before they are invented over languages that make inventions obsolete.

 

Mike McKay

XNAT Developer

Mike is a programmer working on XNAT. He completed Bachelor’s degrees in Computer Science, Math, and Political Science at the University of Maryland and received a Masters in Political Science from Washington University.

Mike likes to spend his free time watching old movies, reading, debating philosophy with friends, and trying to save the world. He can also recommend the best vegan restaurants in town.

 

XNAT Attendees

Please add or amend your information below. If a small bio isn't enough room to say what you want to say, feel free to create and link to a new page in this wiki and expound away.

  Name Group Brief XNAT-related Bio and/or Workshop Goal Guest Talks Scheduled Contact
  David Cash University College London

Experience: I have been using and customizing XNAT for many years

Current Projects:

  • GENFI 1 and 2 - multi centre studies similar to DIAN
  • RADAR - clinical trial in AD
  • 1946 study- single site ageing study
  • Day 1: Using XNAT to Manage Large Scale Trials in Dementia

 
  Jordi Huguet University of Amsterdam

Experience: I have been using and customizing XNAT for many years

Current Projects:

  • The Dutch Translational Research IT (TraIT) project, aiming to organize, deploy and manage a nationwide long-lasting IT infra for research data.
  • Data management infrastructure for the COBRA European project (7th Framework Program). Collaboration with the Computational, Cognitive and Clinical Neuroimaging Laboratory of the Imperial College London.
  • ICT infrastructure for managing/processing/analyzing neuroimaging-related research data at the Spinoza Centre for Neuroimaging, The Netherlands.
  • Data management at the Biomarker Discovery through Deep Learning (BiDDLe) project. 
  • e-Science Gateway project, a science gateway for biomedical data analysis on the Dutch national grid infrastructure. Implemented and deployed for the computational neuroscience research community as the Neuroscience Gateway.
  • Day 1: Using XNAT at the University of Amsterdam

 
  Matt South Oxford University

Experience: I've been tending two research focussed xnat instances over the last twelve months in a DevOps role.

Current Project: Dementias Platform UK

  • Day 1: DPUK - A Distributed Network of XNAT Installations

 
  Simon Doran CRUK Cancer Imaging Centre at the Institute of Cancer Research

Experience: I have been using and customizing XNAT for many years

Current Project:  Three principal XNAT platforms implemented:

  • XNAT_identifiable (clinical imaging with full PHI, within hospital firewall); 
  • XNAT_anonymised (research imaging data); 
  • XNAT_CRUK (prototype national image repository for the UK cancer community).
  • Day 2: XNAT in Cancer Diagnosis, Therapy and Research

 
  Jonathan Passerat-Palmbach Imperial College

Experience: I've been playing with it for a while at different levels (build, user interface, API), but no production instance yet.

Current Project: We plan to host a private and a public to manage and share the data collected over the developing Human Connectome Project (http://www.developingconnectome.org/project/). In the same time, I'm trying to provide a simple access to the OpenMOLE pipeline management system (http://www.openmole.org/) for XNAT users.

  • Day 3: OpenMOLE

j.passerat-palmbach@imperial.ac.uk
  Daniel Beasley University College London

Experience: I've been working with XNAT for a couple of years.

Current Projects:

  • Dementia Research Center, UCL (1946 and LIFTD)
  • BRC Imaging Initiative, large scale clinical data, National Neurological Hospital/UCL.

  • Day 3: XNAT for Large Scale Clinical Data

 
  David Just Mayo Clinic

Experience: I have been using and customizing XNAT for many years. Currently acting as primary maintainer for pyXNAT.

Current Projects: Multiple multi-center clinical trials and research projects at the Mayo Clinic Aging and Dementia Imaging Research Laboratory (ADIR)

Running five XNAT instances with multiple customized data types.

  • Day 4: Python for XNAT

 
  Hakim Achterberg Biomedical Imaging Group Rotterdam

Experience: I have been running one or more studies on XNAT for the last year or so

Current Project: Multiple in-house and multi-center studies

  • Day 4: Python for XNAT

 
  James Dickson Radiologics

Experience: Managed and customized multiple XNAT instances for both research and clinical environments.

Current Project: Working on a number of XNAT/XNATCR projects for Radiologics.

  • Day 4: Dynamic DICOM Anonymization

 
  Kate Alpert Northwestern University

Experience: I have been using and customizing XNAT for many years. Outside of the office, I'm likely to be found skiing, mountain biking, climbing, or running.

Current project: Northwestern University Neuroimaging Data Archive (NUNDA) - some administration and lots of pipeline development/customization.

   
  Mark Bergman CBICA, University of Pennsylvania

Experience: I have been running one or more studies on XNAT for the last year or so

Current Project: Currently receiving data automatically from clinical PACS, manually for ~5 projects. Would like to add more automated pipelines, integration with SGE, and automated cryptographic anonymization via GDCM.

   
  Aniqa Arif New York State Psychiatric Institute/ Columbia Psychiatry

Experience: I have been using and customizing XNAT for the last year or so.

Current Project: We have implemented and manage an institute-wide production instance, XNAT@NYSPI used exclusively for MR sessions. Currently we have about 95 studies and 2000 or so imaging sessions. We have XNAT integrated with our processing cluster (running Grid Engine) that queues and runs the automated pipelines.

   
  Brian Boyd Vanderbilt University

Experience: I have been using and customizing XNAT for many years.

Current Project: Our XNAT is a campus-wide collaborative effort that I help support. My lab does research in several psychiatric illnesses.

   
  Richard Barcus Wake Forest University Baptist Medical Center

Experience: I have downloaded and installed XNAT, but am just getting started.

Current Project: I am learning XNAT with the goal of maintaining the ANSIR Lab at WFUBMC.

  rbarcus@wakehealth.edu
  Monika Mellem BlackThorn Therapeutics

Experience: I have never used XNAT before

Current Project: Examining functional networks in large fmri datasets (and maybe eeg/meg)

   
  Tom Close Monash Biomedical Imaging, Monash University

Experience: I have downloaded and installed XNAT, but am just getting started

Current Project: All projects associated with Monash Biomedical Imaging

   
  Benjamin Yvernault University College London

Experience: I have been using and customizing XNAT for many years.

Current Project: I am working on different XNAT installations for various projects:

  • CMIC-XNAT : XNAT for CMIC data at UCL
  • Prostate-xnat: prostate cancer imaging at UCL
  • epinav-xnat: XNAT instances for epilepsi surgical plans
  • qs-control: queen square control data using XNAT
  • XNAT_CRUK (prototype national image repository for the UK cancer community) - Working with Simon Doran.
   
  Ben Wagner ANSIR Lab at UT Southwestern

Experience: I have been using and customizing XNAT for many years

Current Project:

  • iTAKL-Youth (5R01NS082453 NINDS, 5R03NS088082 NINDS)
  • iTAKL-High School (5R01NS091602 NINDS)
  • AA-DHS Mind (5R01NS075107 NINDS)
  • DHS Mind (5R01NS058700 NINDS) 

We also have several smaller studies with collaborators within UTSW and at Wake Forest Baptist Medical Center.

   
  Georg Winterer Pharmaimage Biomarker Solutions GMBH

Experience: I have downloaded and installed XNAT, but am just getting started

Current Project: Biocog eu-funded imaging study

   
  Mark Shanaman McKesson

Experience: I have downloaded and installed XNAT, but am just getting started

Current Project: Supporting McKesson PACS users who have expressed interest in a research management application.

   
  Ernest Scalzetti SUNY Upstate Medical University, Department of Radiology

Experience: I have never used XNAT before

Current Project: A registry of patients who had CT scans for pulmonary embolism, including images and clinical information

   
  Sanket Gupte NIH/NIDA
NIH/NIAAA
NIH/NIMH

Experience: I attended the last XNAT workshop in St. Louis , and that was the first time I came to know of it's existence as well as awesomeness.
Current Project: Besides other things, Have been working on developing extensions/customizations to XNAT for three Neuroimaging Branches of NIDA, NIAAA and NIMH at the NIH. Also develop other processing/analysis scripts/applications, sometimes involving Xnat. (smile)

   
  Gunnar Schaefer

Stanford University

Flywheel

Not an active XNAT user. Lead developer and chief architect of the SciTran project. Also, VP of Engineering at Flywheel.

 
  John West Indiana University Center for Neuroimaging

Experience: I have been running one or more studies on XNAT the last year or so.

Current Projects:

1) Indiana Imaging and Biomarker Neurorepository -  combines neuroimaging, biomarkers, and EMR data for research purposes.

2) Indiana Alzheimer Disease Center  - used for storing research scans from IADC.

   
  Pratik Gandhi Indiana University Center for Neuroimaging

Experience: I have been running one or more studies on XNAT the last year or so.

Current Projects:

1) Indiana Imaging and Biomarker Neurorepository -  combines neuroimaging, biomarkers, and EMR data for research purposes.

2) Indiana Alzheimer Disease Center  - used for storing research scans from IADC.

 
  Tina Guan

University of Washington

MR Research/Brain Imaging Center

Experience: I have been running one server with many studies on XNAT for last year or so, including multi-center studies.

Current Project: All projects associated with MR Brain Imaging Center

 
  Ravi Tripathi

University of Alabama at Birrmingham

Visual Brain Core

Experience: I have downloaded and installed XNAT, but am just getting started

   
  Brad Zoltick NIH/NIMH, Bethesda, MD

 

Experience: I have worked with an earlier version of XNAT. 

Current Project: Move a large archive of neuroimaging data sets consisting of structural MRI, fMRI, MRS and DTI, with its associated demographics and the subject's cognitive performance data, into XNAT.  Very interested in the Python interface (pyXNAT) to XNAT.

   
  Spiro Pantazatos New York State Psychiatric Institute/ Columbia Psychiatry

Experience: I am relatively new to XNAT.

Current Project: Considering XNAT to manage integration and mega-analyses of large publicly available MRI and fMRI data sources. Also interested in pyXNAT.

  spiropan@gmail.com
  Eve LoCastro Weill Cornell Medical College

Experience: I have been running XNAT on standalone servers since v1.6.3

Current Project: I have been developing image post-processing routines and report generation via XNAT's pipeline automation. Also using XNAT to assist in storing non-DICOM-standard formats to supplement PACS limitations.

 
  Chad Jackson University of Pennsylvania - Neuropsychiatry Section Experience: Customization, pipeline building, and support of an XNAT installation for the last 5 years.    
  Mike Kerich NIH/NIAAA

Experience: Help manager our XNAT server on a linux platform for last 2 years.

Current: Back filling old data. Finding ways to integrate XNAT data with other subject characterization information and psychological/physiological data.

   
  Stephen Damon Vanderbilt University

Experience: Admin for several years. Database backend experience (psycopg2) for a year.

Current Project: Vanderbilt's ImageVU (BioVU extension project). We plan to funnel ~30% of the hospital PACS into a simple queryable system and send data to XNAT for automated processing using DAX, our homegrown processing engine. I also support about 60 active projects with over 160 different pipelines.

Day 4  

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