Recommended amount of resting BOLD for brain network estability

[Estephan Moana]

Hello, I'm planning a new study of adults (18+ yrs) that will include resting BOLD scans before and after 7 days of local heat application to the face to assess any changes in brain resting state (full brain, selected networks). I'm planning to use the HCP Lifespan Aging protocol:

• Spin echo fieldmaps (AP, PA)
• BOLD resting state: run 1 AP, run 2 PA (each scan: resolution = 2mm isotropic, 488 volumes, duration: 6min41s)
• T1w (multiecho MPRAGE, duration: 8min22s)
• T2w (SPACE, duration 6min35s)

I will use the HCP pipelines to process these data. I remember that in the past the advice was to collect as much BOLD data as possible for signal stability (up to 30 min). My questions are: 

1. Is the above protocol sufficient for full use of the best features of the HCP pipelines, including enough BOLD data?
2. Assuming our focus is the BOLD data, if we need to reduce scanning time can we shorten the T1w and/or T2w scan durations?

Thank you.

Estephan

[Glasser, Matthew]

Hi Estephan,

 

If you are starting a new study, I would make a number of changes:

 

1. I would collect equal amounts of fMRI in both phase encoding directions (you can adjust the run length and number of runs to fit in your time block).
2. I would get 2.4mm isotropic fMRI data with TR=1s, flip angle = 60 degrees, 60 slices, MB=4.  This will give you a bit better SNR in the center of the brain.
3. I would get SE fieldmaps that match the fMRI.  Remember also to save out the SBRef from the fMRI.
4. I would still get 0.8mm isotropic T1w and T2w, as that improves the surface quality a lot over 1mm.
5. I would use a single echo MPRAGE with TR=2400, TI=1000, FA=8 degrees, TE= minimum.  If you wanted to shorten the time, you might be able to push IPAT to 3.
6. For T2w SPACE if you used compressed sensing (e.g., CS=4) you could shorten that quite a bit.
7. I would turn PreScan normalize on for everything.

 

Matt.

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[Harms, Michael]

 

RE 2/3: If you change the spatial resolution on the fMRI and SE fieldmaps, you'll want to re-optimize the echo spacing (ES).  That means find the Bandwidth that yields the lowest ES for the fMRI scan with revised spatial resolution, and then decrease the BW so that the ES increases by 1-2 "ticks" so as to avoid stimulation limit problems at run-time.  Then set the SE fieldmaps (with matching spatial resolution) to match the fMRI ES and Bandwidth exactly, by setting them to use the same BW and turning On the "Free Echo Spacing" option so that you can directly enter the exact same ES as the fMRI.  (Otherwise, without use of the "Free echo spacing" option, the SE fieldmaps will typically have a slightly different ES for a given BW value).

 

Cheers,

-MH

 

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Michael Harms, Ph.D.

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Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.                        Tel: 314-747-6173

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[Glasser, Matthew]

We still need to compute a curve to guide these kinds of questions for each application.  Get as much as is feasible.  The curve is very sharp to begin with and then will slowly plateau.

Matt.

 

From: Estephan Moana <esteph...@gmail.com>
Date: Wednesday, September 3, 2025 at 1:11 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Glasser, Matthew" <glas...@wustl.edu>
Subject: Re: [hcp-users] Recommended amount of resting BOLD for brain network estability

 

Great, thanks for the detailed advice Matt. Is there a bare minimum amount of BOLD data that I should not go below, in terms of scan duration and/or volumes acquired?

[Glasser, Matthew]

Do you have Terra.X?  Recommended fMRI resolution for 7T is 1.6mm isotropic TR=1s, MB=5, IPAT=2, FA=Ernst Angle…

 

Think of trying to maximize the amount of fMRI, not minimize it.  Obviously, you can only do what you can do, but under 30 minutes more is definitely better.

Matt.

 

From: Estephan Moana <esteph...@gmail.com>

Date: Wednesday, September 3, 2025 at 1:23 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Glasser, Matthew" <glas...@wustl.edu>

Subject: Re: [hcp-users] Recommended amount of resting BOLD for brain network estability

 

Thanks for the detailed advice Matt. Follow-up questions:

1. I should have mentioned that we plan to acquire these data in the 3T Prisma and the 7T Terra systems. Would this change anything in your recommendations?
2. What would be the minimum amount of BOLD data needed for reasonable data quality in terms of scan duration or volumes acquired?

Thank you.

 

Estephan

 

On Wednesday, September 3, 2025 at 12:34:51 PM UTC-5 glas...@wustl.edu wrote:

[Estephan Moana]

Great, thanks for the detailed advice Matt. Is there a bare minimum amount of BOLD data that I should not go below, in terms of scan duration and/or volumes acquired?

On Wednesday, September 3, 2025 at 12:34:51 PM UTC-5 glas...@wustl.edu wrote:

[Estephan Moana]

Thanks for the detailed advice Matt. Follow-up questions:

1. I should have mentioned that we plan to acquire these data in the 3T Prisma and the 7T Terra systems. Would this change anything in your recommendations?
2. What would be the minimum amount of BOLD data needed for reasonable data quality in terms of scan duration or volumes acquired?

Thank you.

Estephan

On Wednesday, September 3, 2025 at 12:34:51 PM UTC-5 glas...@wustl.edu wrote: