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Software Engineer, Research

Charlestown, Massachusetts Massachusetts General Hospital

Software Engineer, Research


The Software Engineer is responsible for maintaining and developing the FreeSurfer software package across multiple platforms (Linux, Mac, and Windows). S/he will work closely with researchers and other software engineers to build, improve, test, support, and document the software. The Software Engineer reports to the Director of LCN, the Principal Investigator of the FreeSurfer Maintenance grant, and the Research Lab Manager.

The position requires strong written and verbal communication skills and the ability to be proactive and work independently.

The FreeSurfer software package, produced by the Lab for Computational Neuroimaging (LCN), is a multi-platform suite of software tools for the analysis of brain imaging data in use by thousands of neuroscientists, engineers and clinicians around the world. It has been critical for basic neuroscientific advances in our understanding of the brain, as well as more accurately and sensitively quantifying the effects of disease processes such as Alzheimer’s disease, schizophrenia, autism, and Huntington’s disease among others. The Martinos Center for Biomedical Imaging at the Massachusetts General Hospital (MGH), affiliated with both Harvard Medical School and MIT, is one of the premier brain imaging centers in the world.


Development responsibilities include:

Develop new neuroimaging algorithms in Python and C++

Refactor, optimize, and clean existing algorithms and frameworks in Python and C++

Develop and integrate a FreeSurfer python framework with previous tools

Test responsibilities include:
Develop and execute software test plans, like unit and regression tests on multiple platforms
Monitor automated tests, analyze test results, and recommend corrective action

Maintenance and support responsibilities include:

Assist in bug-fixing and feature enhancement

Maintain open-source availability on GitHub

Help resolve multi-platform compatibility, installation, and run-time issues
Monitor the FreeSurfer mailing list and respond to end-user issues

Maintain and upgrade the Freesurfer mailing list and website
Assist with FreeSurfer training courses

Teaching responsibilities include:

FreeSurfer classes locally and abroad

One-on-one instruction with faculty and staff

Documentation responsibilities consist primarily of maintaining and contributing to the FreeSurfer documentation website.


– 3-5 years of C/C++ and Python programming experience in a Unix environment is required. Unpaid experience is accepted.
– Experience with neuroimaging analysis a plus
– Basic shell scripting experience is desired
– Advanced knowledge of Git and GitHub version control software
– Experience with the software development life cycle and methodologies
– Deep learning experience is a plus – preferably using Tensorflow Keras or PyTorch


Position involves working in a fast-paced Computational Neuroimaging Lab. The lab develops and maintains software for MR image analysis and is responsible for several in vivo and ex vivo (human) MRI projects. The employee will work in a general office environment alongside Harvard University faculty, postdoctoral fellows, Research Technicians, and students. The lab is composed of members from a wide range of backgrounds (engineering, neuroscience, computer science, math, physics, psychology & biology).

EDUCATION: Bachelor’s Degree
Field of Study/Additional Specialized Training: Computer Science. Knowledge of neuroscience, psychology, or cognitive science is a plus.

C/C++ Programming Experience: minimum 2 years

Python Programming Experience: minimum 1 year

Experience in LINUX environment: minimum 2 years

. Git and Git Hub Experience: minimum 1 year

Massachusetts General Hospital is an Equal Opportunity Employer. By embracing diverse skills, perspectives and ideas, we choose to lead. Applications from protected veterans and individuals with disabilities are strongly encouraged.

MA-Charlestown-MGH 13th Street

MGH 13th Street (MGHCharlestownBldg149)
149 13th Street
Charlestown, 02129

MGH 13th Street

149 13th Street


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