HCP Protocols

[Alishba Sadiq]

Hi,

 

I am working on a resting state fMRI data for functional connectivity analysis. In the fMRI folder, I have four files for two runs with RL and LR encoding. I would like to know How can we use them? Which one to use.

Either these are just runs or different sessions acquired at two different time instances.

 

Please assist.

Thank you.

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UT Southwestern

Medical Center

The future of medicine, today.

[Tim Coalson]

The Young Adult S1200 release reference manual, under "resting-state fMRI", says:

rfMRI data were acquired in four runs of approximately 15 minutes each, two runs in one
session and two in another session, with eyes open with relaxed fixation on a projected bright
cross-hair on a dark background (and presented in a darkened room). Within each session,
oblique axial acquisitions alternated between phase encoding in a right-to-left (RL) direction in
one run and phase encoding in a left-to-right (LR) direction in the other run.

PDF links on the right, here:

https://www.humanconnectome.org/study/hcp-young-adult/document/1200-subjects-data-release

If this isn't the right dataset, there are probably release notes elsewhere for the data you are using.

We recommend using the versions with at least FIX denoising and MSMAll registration (_clean.dtseries.nii).  You can concatenate them within a subject as long as you at least demean them first, instructions in FAQ #3, here: https://humanconnectome.github.io/HCP-Wiki/docs/HCP%20Users%20FAQ.html

Tim

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[Alishba Sadiq]

Thank you for your email. 

So, I can concatenate all four runs after the demean process, or I can concatenate just LR and RL for each session?

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Alishba Sadiq, PhD

Postdoctoral research fellow

Department of Diagnostic Radiology & Nuclear 

Medicine

University of Maryland School of Medicine 

670 W Baltimore St,

21201, MD

+1-667-391-5233

[Glasser, Matt]

I would demean and variance normalize the runs.  In the future, this will be done for users, as it generates so many questions.

Matt.

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[Glasser, Matt]

All runs.

Matt.