NTRC - For Investigators

Housed within the Department of Psychiatry and Behavioral Sciences' Nancy Friend Pritzker Psychiatry Building at Mission Bay, the Neuroimaging Technology Research Center (NTRC) is run by the Department of Radiology, under the leadership of Leo Sugrue, MD PhD, as a collaborative effort between the Departments of Radiology, Psychiatry & Behavioral Sciences, Neurology, and Neurosurgery.

The center’s goal is to pioneer the application of advanced brain imaging and image-guided therapy in the diagnosis and treatment of neuropsychiatric disease. The NTRC has two next generation 3T Siemens Cima.X MRI scanners with gradients optimized for advanced neuroimaging applications, as well as neuromodulation suites for focused ultrasound and transcranial magnetic stimulation.

Getting started with NTRC scanner reservations

Follow these steps to reserve scanner time at the Neuroimaging Technology Research Center (NTRC):

Step 1: Submit your study application

Begin by submitting your imaging protocol and study details through the Full Study Application Process. The NTRC committee reviews applications monthly but can arrange ad hoc reviews for urgent requests.

Access the application form here: Full Study Application Process

Step 2: Approval and reservation instructions

After your application is reviewed, you will receive:

• An official approval letter.

• Detailed instructions on reserving scanner time.

Note: Your approval letter and study ID (ART#) are required to schedule MRI scanner time.

For additional information on reservations, cancellations, and site/parking details, refer to the Radiology Research Scheduling Guide (PDF).

Scanner recharge rate

The following table outlines the costs associated with using the NTRC scanners. Rates are provided for both internal and external users, with details on the applicable units and the effective dates for any rate changes. Please note that rates are subject to change without notice. For the most current rates, please refer to the rate reference link. (Lines 61 – 68)

Step 3. Data Retrieval, Storage and Computing Infrastructure

NTRC Specific - Flywheel

A core goal of the NTRC is to provide its investigators with easy access to standard data pre-processing and QC tools, basic analysis pipelines, and long-term data storage/curation via a centralized process that provides data provenance tracking and reproducibility. To this end the NTRC is partnering with Flywheel (https://flywheel.io/), a neuroimaging informatics platform that securely stores and organizes imaging data in encrypted cloud storage and provides web-based, command-line, and Python API tools for data search, organization, transfer, preprocessing, and analysis. After anonymization, all research brain imaging data collected at NTRC will be uploaded to Flywheel. For all studies Flywheel will provide basic QC tools to assess image quality, ‘gears’ to perform basic preprocessing of functional and diffusion MRI (using standard packages like fMRIPrep and QSIPrep), and long-term cloud-based data archiving to ensure a permanent repository of all collected data. Flywheel has extensive additional functionality in the form of custom gears for image processing and data analysis that can use either local HPC or cloud-based computing resources. However, individual investigators will have to pay for costs associated with this additional functionality through their own Flywheel accounts. We believe that Flywheel represents the best current solution for NTRC’s data processing, curation, and storage goals but the NTRC Scientific Steering Committee will actively evaluate the success of Flywheel in meeting these goals.

Automated Image Retrieval (AIR)

AIR is a self-service platform for accessing clinical and research imaging data. It automates the deidentification of image headers but requires users to manually review and remove Protected Health Information (PHI) from pixel data. AIR is best for researchers who need quick access and are comfortable managing their own data transfer workflows.

For detailed information, visit the AIR Services page.

Full-Service Data Transfer (CRCs)

The Radiology Clinical Research Coordinators (CRCs) provide a full-service solution for data transfer, including deidentification, regulatory support, and technical assistance. This service is ideal for researchers seeking comprehensive support from data retrieval to delivery.

For comprehensive details, visit the Full-Service Data Transfer page.

Comparison: AIR vs. Full-Service Data Transfer

Scientific Computing Services (SCS)

UCSF’s Scientific Computing Services (SCS) complements AIR and CRC services by providing:

• High-performance computing clusters for large-scale data analysis.

• Secure, scalable storage for research data.

• Expert consulting for custom workflows.

These services empower researchers to process and analyze imaging data efficiently while ensuring compliance with UCSF's data security and privacy standards.

For additional information, explore Biomedical Imaging Research Support Services.

Data Retrieval, Storage, and Computing Infrastructure: Service Rates

The following table provides a breakdown of the rates for services related to data retrieval, storage, and scientific computing infrastructure available at UCSF. These rates apply to both internal and external users, with details on the applicable units and the effective date for any rate changes. Please note that rates are subject to change without notice. For the most current rates, please refer to the rate reference link.