21-001046 - Draft SOW.pdf

OpenNeuroPET

DRAFT

STATEMENT OF WORK (SERVICES)

(SOW)

GENERAL INFORMATION

Title of Project:

PET Analysis Pipeline and Molecular Imaging Brain Atlas

Statement of Need and Purpose:

In recent years, the importance of data sharing has increasingly been recognized by the neuroimaging community because of the poor replicability of findings, the need for appropriate quality control, the greater statistical power provided by larger samples, and the higher scientific impact of multilateral collaborations. In addition, our funding bodies and scientific journals increasingly require that the data be shared.

The NIMH IRP plans to establish an archive for human brain data acquired with positron emission tomography (PET), as no such archive currently exists. This new archive will be called OpenNeuroPET and will be an extension of OpenNeuro, which is funded by NIMH but is currently limited to magnetic resonance imaging (MRI) data. The proposed archive will follow the recommendations of international leaders in the PET field and be capable of communicating and synergizing with other datasets and imaging modalities.

At its recent biennial meeting in July 2018, the NeuroReceptor Mapping community of over 300 attendees supported the recommendations of the committee and voted unanimously that we finalize recommendations for standardizing PET and establish an archive based on those recommendations. The paper was titled, “Guidelines for Content and Format of PET Brain Data in Publications and in Archives” and has been published in J. Cereb. Blood Flow and Metab. 2020. This proposed contract will provide expert services to the NIMH IRP to establish and maintain an archive based on those guidelines.

The OpenNeuroPET Archive will synergize with NIH’s BRAIN Initiative (Brain Initiative through Advancing Innovative Neurotechnologies) in two important ways. First, it will follow the Brain Imaging Data Structure (BIDS) format proposed under the BRAIN Initiative. Second, it will establish software that allows the larger MRI/fMRI community to collaborate with the smaller PET community.

This proposed contract will provide expert services to the NIMH IRP: 1) to propose a data analysis pipeline that PET centers can use to reliably produce individual PET and MR images and 2) to create average PET images of each submitted data set, called a Molecular Imaging Brain Atlas (MIBA).

https://openneuro.org/ https://braininitiative.nih.gov/

Background Information and Objective:

The general purpose is to establish an international archive for PET data so they may be meaningfully and freely shared. The awarded contractor will help with the following two objectives:

Objective 1: To recommend a data analysis pipeline to create uniform PET and MRI images that can be shared and averaged. Because there is no agreed upon "right way" to process PET data, we will have a processing stream that allows flexibility and adaptability.

While most PET data are analyzed on a region of interest (ROI) basis, most MRI data are analyzed on a voxel-wise (i.e., map) basis; thus, we need a processing stream that can do both.

We will base the stream on PETsurfer (15, 16), the PET analysis module of the FreeSurfer suite of neuroimaging tools. FreeSurfer is an MRI analysis stream that provides detailed anatomical segmentation of an individual's brain, including a surface-based representation of the cortical surfaces. It provides the ROIs for the ROI analysis as well as intersubject registration to the fsaverage surface space for voxel-wise analysis. It can also render results in the MNI152 volume space to facilitate integration with FSL, SPM, and AFNI. PETsurfer is built on top of FreeSurfer and provides kinetic modeling and partial volume correction. The basic steps will consist of the following: FS analysis of the T1-weighted MRI (with MRI scanner distortion correction (17)); motion correction of the PET time series (18); registration of PET to MRI (19, 20); partial volume correction (15, 16, 21, 22) (or not); resampling the PET data into ROIs, MNI152 space, and/or FreeSurfer surface space; spatial smoothing; kinetic modeling (if needed, using Logan (23) (invasive or reference), Patlak (24) (invasive or reference), or multilinear reference tissue model (MRTM) 1 or 2 (25, 26)); and, finally, group averaging to create the MIBAs.

Objective 2: To create molecular imaging brain atlases. These atlases will provide the average molecular target densities in the brains of healthy human subjects as quantified by in vivo PET. The molecular imaging brain atlases will be offered in formats that facilitate inclusion in MRI analyses, thus greatly expanding their potential impact. The OpenNeuroPET Archive will serve as the platform for aggregating already-collected data for dozens or hundreds of different molecular targets, thereby allowing a comprehensive characterization of, for example, the neuroreceptor signature of the human brain. The proposed MIBAs would be analogous to the Allen Human Brain Atlas (14), which reports the regional distribution in postmortem human brain of the densities of gene transcripts and expressed proteins for over 400 genes. This atlas has been widely praised, used by diverse fields, and cited as a data source by over 2,000 publications since 2005.

As a rough overview, during the first year, the contractor will create a standard data analysis pipeline. During the remaining four years of the award, the contractor will create the brain atlases for each submitted data set.

Period of Performance:

The period of performance is one 12-month base year with four 12-month option years.

SCOPE OF WORK

General Requirements:

- Independently and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government, as needed to perform the Statement of Work below.

Specific Requirements:

To perform the work, the contractor must meet the following criteria:

- Be intimately familiar with the Guidelines paper on the content and format of brain PET data;

- Be thoroughly knowledgeable of the OpenNeuro platform;

- Be widely recognized by and familiar with the Brain PET and MRI communities so as to advocate and educate the communities to use the proposed archive;

- Have significant experience with brain data archives;

- Have recognized expertise in the analysis of brain PET data;

- Have recognized expertise in the analysis of brain MRI data;

- Have recognized expertise in the integration of PET and MRI data;

- Be intimately familiar with the analysis of MRI and PET data on the cortical surface;

- Have experience in the development, testing, dissemination, training, and support of brain analysis pipelines; and

- Have experience in the development and dissemination of brain atlases.

LEVEL OF EFFORT:

We expect the proposed work will require at least one full-time research assistant, 55% of a software engineer, and 25% effort of a PET expert. Each of the first two years will need additional funds to purchase computers and electronic storage.

GOVERNMENT RESPONSIBILITIES

There will be no Government Furnished Equipment as part of this Purchase Order. The PI at NIMH will oversee the progress, as demonstrated in monthly meetings and annual reports.

DELIVERY OR DELIVERABLES

• In the first year, the contractor will create a PET analysis stream to be applied to the data uploaded to OpenNeuroPET. The software will create BIDS-compatible output and meet the standards to the Guidelines paper. Analyses will be done in the volume, on the cortical surface, and in regions-of-interest. The pipeline will include tools for PET-MRI registration, MRI gradient distortion correction, kinetic modeling, and PET partial volume correction. The pipeline will be integrated and distributed with the FreeSurfer neuroimaging analysis package.

• In the second year, the contractor will vet the analysis stream with the PET community to receive feedback about features or modifications to the stream. The contractor will begin to create molecular imaging brain atlases (MIBAs) by applying the stream to the data uploaded to OpenNeuroPET from other sources (expecting 100 PET data sets from at least five different PET centers).

• For the last three years of the award, the contractor will: (1) Create MIBAs from the data uploaded to OpenNeuroPET. The data analyzed will have both PET and T1-weighted MRI; the MRI must be of sufficient quality to extract cortical surface models; the quality will be assessed by the contractor. The contractor will not be expected to analyze more than 150 cases per year; it may be less if uploaded data is not of sufficient quality or not enough data have been uploaded to the archive. (2) Make the MIBAs publicly available to the neuroimaging community through OpenNeuroPET, creating a digital object identifier (DOI) for each MIBA. (3) Train the international PET community on the use of the processing stream and MIBAs and make modifications based on feedback, under overall direction of the NIMH IRP. The contractor will also provide a Helpdesk for users.

REPORTING REQUIREMENTS

Written Documentation: Each annual report will thoroughly document progress made in the prior year, including but not limited to:

- Overview of accomplishments made on the two overall objectives (see above).

- Detailed description of tasks accomplished.

- Documentation of progress made – e.g., software code, number of scans deposited, or number of investigators who have been helped.

Conference calls: Communication will occur through regular email contact, and/or monthly conference calls with the PI as needed. Monthly calls will be organized by NIMH. These calls will be held to understand progress, to identify problems, and to resolve them.

END RESULTS/ DELIVERABLES

The following table describes 1) the products and tangible end results that are expected from each task contained in the specific requirement; 2) the date each deliverable is due; and 3) the Government acceptance criteria. All days are business days unless otherwise specified.

End Result/Deliverable

Due Date Acceptance Criteria

Presentation of PET analysis stream and MIBAs at one research conference per year

During each of the last three years of the award.

The Principal Investigator will review and provide acceptance and/or feedback within 10 days of each presentation.

Create MIBAs from 300 cases uploaded to OpenNeuroPET

By end of third year. The Principal Investigator will review and provide acceptance and/or feedback.

Instruct and assist the PET community to use the PET analysis stream and the MIBAs. Creation of new MIBAs from 600 cases uploaded to OpenNeuroPET

During last three years of the award.

The Principal Investigator will review and provide acceptance and/or feedback.

Annual Report

Within 60 days of the end of each year.

The final report will be accurate, complete, submitted on time, and be prepared in accordance with the Reporting Requirements section. The Principal Investigator will review and provide acceptance and/or feedback within 10 days of receipt.

OTHER CONSIDERATIONS

Travel:

The contractor must send personnel to international brain imaging meetings during at least the last three years of the award, if not sooner.

Key Personnel:

All key personnel will be hired by the contractor.

Data Rights:

The results / data generated on this contract will be made publicly available on OpenNeuroPET and may be distributed with FreeSurfer or other software packages. Software and algorithms developed as part of this grant, including Free Surfer and PETSurfer, will remain entirely owned by MGH.

Section 508—Electronic and Information Technology Standards:

The contractor shall comply with Section 508 of the Rehabilitation Act (29 U.S.C. § 794d), as amended by the Workforce Investment Act of 1998 (P.L. 105-220), August 7, 1998.

Publications and Publicity:

Users of the website will be free to write papers based on data in the proposed archive and need not be include the contractor(s) as coauthor(s).

Confidentiality of Information:

The Contractor(s) will not receive, and therefore will not be able to distribute, any data sensitive to the operation of the federal government, nor any personal identifying information about individuals.