Setting up a FreeSurfer Worker Node on Azure

Acknowledgements: Thanks to Azure guru Peter Barrera at Microsoft for setting up the infrastructure. And thanks to Ezra Wegbreit at PediMind and Ryan Cabeen for their expertise with Freesurfer.

If you need to do neuro MR post-processing, but don't have access to a high performance computing cluster, it's ...


On November 6th and 7th, 2014, Rhode Island Hospital will be hosting the first Conformal Thermal Ablation Research Network workshop. This workshop will bring together leading experts on ablation therapy to discuss novel treatment planning procedures. With demonstrations at both the hospital and Brown University, it aims to foster collaboration ...

Cancer Ablation Research at Rhode Island Hospital

When Mrs. Hope Tucker's brother contracted lung cancer, she watched in horror as his unsuccessful surgery to remove the tumor left him tied to an oxygen machine. In the end, it only increased his suffering during his last few weeks. So when she was also diagnosed with lung cancer, she chose a different approach.

Computer Vision and Image Analysis Research Update 10/23/14

Tung, Smith, Merck


  • Fall R21 for ablation planning project in prep
    • Basically just budget and finalize approach left
  • Summer industry mtbi project site visit happened, moving ahead
  • Image fusion for DBS (Assad) ramping up
    • Collins working w med student on data review and using Velocity (registration software) to directly ...

Lifespan Annual Research Celebration


I presented a poster at the Lifespan Annual Research Celebration on the preliminary results from MUSTACHE. You can find the abstract published online here.


Research update: Not much happened in the last few weeks. I've been fixing bugs in the original MUSTACHE code and writing up the research proposal ...

Translational Research Workflow and Tools

At any given time, the 3D Lab has 3-5 students, RAs, and technologists working with a half a dozen collaborators across the hospital and Brown on multiple projects. I do very little actual science anymore; I mostly organize research projects. So I have become increasingly interested in academic productivity and ...

Ultrasonography Research Update


So far, I've been working on pulling together all the pieces of MUSTACHE. Updates to that project include:

  • Organizing the data so each rater has one mask for each patient, and each patient is rated by both raters
  • Creating a GUI for manual raters to classify steatosis images ...

3D Lab Website Development

Back in the day, I was a web developer. I actually learned how to program because I was too lazy to copy and paste footers, so I ended up writing my own parsers to read marked up text files into a sql database where I could use it to dynamically ...

3D Face Capture

Merck 3D Face

I am putting together a strategy for creating a bust of a donor who is supporting our tech build out. My idea is to do a 3D capture of their head and then fabricate it with the 3D printing hardware at Prince Labs.

Dr. Stephen Sullivan demoed the Canfield Vectra ...

Computer Vision and Image Analysis Research Update 7/22/14


  • Ablation planning project awarded a Brown University DEANs grant (Merck, Kimia, Dupuy)
  • Fall R21 for ablation planning project in prep
  • Fall? K (L Merck) for hydrocephalus in prep


  • 4 manuscripts in prep: 2xAblation (Deshazer, Cook/Glidden), endoscopy (Fallon), u/s shape modeling for stenostosis (DeFreitas)
  • 2 abstracts in ...

3D Printing from CT

Skull Model

This was a proof-of-concept for Dr. Taylor and Dr. Sullivan to demonstrate that we could fabricate a 3D model from a CT scan. The skull was extracted as an isosurface from a pediatric head CT and processed with TeraRecon to generate an .stl model. Brian Corkum at Prince Lab printed ...

Thermal Ablation Simulation Research Plan Spring 2014

Garron Deshazer with Dr. Derek Merck, Dr. Damian Dupuy, Dr. Edward Walsh, Dr. Jeom Soon Kim, Dr. William Park


Model and validate thermal profiles produced by a physically based generative model of various microwave ablation procedures (MWA) and correlate these profiles with 3D ablation zone size and shape.

Importance ...