Statement of Work.pdf

January 17, 2021

OpenNeuroPET

STATEMENT OF WORK (SERVICES)

(SOW)

1. 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 (1) 12-month base year with four (4) 12-month option periods.

Place of Performance:

The place of performance is at the Contractor’s facilities.

2. SCOPE OF WORK

2.1. 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.

2.2. Specific Requirements:

The Contractor shall provide services and materials necessary to complete the following tasks:

2.2.1. PET Analysis Stream. In the first year, the contractor shall deliver a PET analysis stream to be applied to the data uploaded to OpenNeuroPET. The software shall read BIDS-compatible input and meet the standards to the Guidelines paper identified in section 7. “References”. Analyses shall be able to be done in the volume, on the cortical surface, and in regions-of-interest. The pipeline shall include tools for PET-MRI registration, MRI gradient distortion correction, kinetic modeling, and PET partial volume correction. The pipeline will be open source and freely available. Contractor shall modify/reprogram FreeSurfer/PETsurfer to meet the goals of the project (e.g., BIDS). In the second year, the contractor shall vet the analysis stream with the PET community to receive feedback about features or modifications to the stream.

2.2.2. PET Analysis Stream Technical Support. The contractor shall provide user support for the analysis stream in several ways.

• First, the contractor shall produce online documentation, including documentation for individual commands, use cases, and tutorials.

• Second, the contractor shall create and man a help desk consisting of an email list or message board where users can post questions about the analysis stream.

• Third, contractor shall provide virtual online or in-peron group training training seminars according to the training schedule listed below. The contractor shall send out the training announcemens thrugh mailing lists frequented by the PET community.

2.2.3. PET Data Analysis. Contractor shall analyze PET and MRI data using the above software package using data from the archive. 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.

2.2.4. Molecular Imaging Brain Atlases (MIBAs). (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;

MIBAs may be made from data not in 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 MIBAs using the mechanism described in “PET Analysis Stream Technical Support”

2.2.5. Quarterly Status Reports (QSRs)

Contractor shall submit one (1) quarterly status report every four months during the period of performance in accordance to the criteria listed in section 6 “Reporting Requirements”.

2.2.6. Annual Reports

Contractor shall submit one (1) annual report each year during the period of performance in accordance to the criteria listed in section 6 “Reporting

Virtual or In-Person Group Training Seminars Schedule

Period of Performance Four (4) Training Sessions

Number of Attendees

Base Period 0 0

Option Period One (1) 1 Not to exceed 50

Option Period Two (2) 1 Not to exceed 50

Option Period Three (3) 1 Not to exceed 50

Option Period Four (4) 1 Not to exceed 50

Requirements”.

2.2.7. Quality Control Plan. The software analysis stream will be subject to a regression test quality control procedure. Once a week, the software will be applied to a representative data set; the results will be compared with a result from when the software was known to be working correctly. Any differences must be tracked down and justified.

- Distribute and support MIBAs to the user community

- Distribute and support modified software to the user community

- Present software and MIBAs at international professional brain imaging meetings

Materials/Equipment needed to complete tasks:

- Two (2) Computers: multi-core large RAM workstations so that multiple data sets can be analyzed at once.

- Digital storage space large enough to hold the large amounts of data needed for the project. We estimate that we will need 10TB of storage. We will use centrally-maintained, mirrored disk space supported by the Martinos Center IT staff to house the data

To perform the work, the contract 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.

3. GOVERNMENT RESPONSIBILITIES

Government – Furnished Information

The Government shall provide sample data sets of brain images to the contractor. All personal identifying information will be removed.

4. REPORTING REQUIREMENTS

Written Documentation:

Quarterly Reports: Each quarterly report shall document progress made, within seven (7) calendar days after the end of each contract quarter. The report shall include: a summary of

Annual Report: Each annual report shall 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 shall 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, identify problems, and resolve them.

5. END RESULTS/ DELIVERABLES

The following table describes 1) the products and tangible end results that are expected from each task contained in section 2.2 “specific requirements”; 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 shall 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 shall review and provide acceptance and/or feedback.

End Result/Deliverable

Due Date Acceptance Criteria

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 shall review and provide acceptance and/or feedback.

Quarterly Status Reports (QSRs) within seven (7) calendar days after the end of each contract quarter

The QSR shall be accurate, complete, submitted on time, and be prepared in accordance with the Reporting Requirements in section 6 and submitted electronically to the Principal Investigator.

The Principal Investigator shall review and provide acceptance and/or feedback within 10 days of receipt.

Annual Reports

Within 60 days of the end of each year.

The final report shall be accurate, complete, submitted on time, and be prepared in accordance with the Reporting Requirements in section 6 and submitted electronically to the Principal Investigator.

The Principal Investigator shall review and provide acceptance and/or feedback within 10 days of receipt.

6. REFERENCES

G.M. Knudsen, 42 middle authors, and R.B. Innis. Guidelines for the content and format of PET brain data in publications and archives: A consensus paper. J. Cereb. Blood Flow Metab 40:1576-1585, 2020. doi.org/10.1177/0271678X20905433.

7. OTHER CONSIDERATIONS

Travel:

The contractor shall send personnel to the yearly Organization of Human Brain Mapping (OHBM) and Neuroreceptor Mapping (NRM) meetings during at least the last three years of the https://doi.org/10.1177%2F0271678X20905433 award, if not sooner. The locations of these meeting vary from year to year; in 2020 they were held virtually due to COVID.

Key Personnel:

All key personnel will be hired by the contractor.

The Contractor employee providing services for this effort shall be considered key personnel. Key Personnel requirements are as follow:

The proposed Key Personnel will become subject to the provisions of Health and Human Services Acquisition Regulation (HHSAR) Clause HHSAR 352.237-75 Key Personnel as follows;

Position

PET Expert

The key personnel specified in this contract are essential to work performance. At least 30 days prior to the contractor voluntarily diverting any of the specified individuals to other programs or contracts the Contractor shall notify the Contracting Officer and shall submit a justification for the diversion or replacement and a request to replace the individual. The request must identify the proposed replacement and provide an explanation of how the replacement's skills, experience, and credentials meet or exceed the requirements of the contract. If the employee of the contractor is terminated for cause or separates from the contractor voluntarily with less than thirty days’ notice, the Contractor shall provide the maximum notice practicable under the circumstances. The Contractor shall not divert, replace, or announce any such change to key personnel without the written consent of the Contracting Officer. The contract will be modified to add or delete key personnel as necessary to reflect the agreement of the parties.

The following individual(s) are essential to the work being performed here under:

Name Title

To be determined in the contract award

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 contract, 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.