HCP-Aging T1w multi-echo MPRAGE unprocessed data

[Yen-Wen Chen]

Dear experts, 

This is my first time to work with HCP data and I would like to work on HCP Aging (2.0 release). I would like to pilot a few subjects with fMRIPrep pipeline and compare with the outputs from the minimally preprocessed data. 

I have some questions about the multi-echo T1w images. 

In the unprocessed package (imagingcollection01/<subject>/unprocessed) T1w folder (T1w_MPR_vNac_4e_e1e2_mean), it has only one .nii.gz, which if I understand it correctly, it's the mean from the 1st and 2nd echo T1w. I am wondering what is the reason that only the first two echoes were used? What about the 3rd and 4th echo? 

If I would like to use the unprocessed T1w, is this *_e1e2_mean.nii.gz the one I should use? Does this mean that I can convert this mean image into conventional BIDS format for T1w (e.g., *_T1w.nii.gz)? 

Or would it be recommended to use the four raw echo data (in OTHER_FILES, *_MPR_vNav_4e_e1.nii.gz, *_MPR_vNav_4e_e2.nii.gz, etc.)? What is the difference between *_MPR_vNav_4e*.nii.gz and *_MPR_vNav_Norm_4e*.nii.gz?

I would appreciate any input or opinion. Thank you.

Sincerely, 

Samantha

[Harms, Michael]

 

Hi,

Please see item (ix) in Section 11.3 of our very recent “Retrospective” on the HCP, where we explain why we are only using the mean of the 1st two echoes for our processing of the HCP-LS MPRAGE data.

https://www.ncbi.nlm.nih.gov/pubmed/34508893

 

“Norm” in a file name indicates that it was “Prescan Normalized” at the scanner.  We are using the “non-Normed” versions (does not include “Norm” as part of file name) for our processing, consistent with what was used for the processing of the HCP-YA data.

 

Cheers,

-MH

 

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

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

St. Louis, MO  63110                          Email: mha...@wustl.edu

 

From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, September 27, 2021 at 12:32 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] HCP-Aging T1w multi-echo MPRAGE unprocessed data

 

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[Yen-Wen Chen]

Hello Michael, 

Thank you for the prompt response and for providing the reference for clarification. It all makes sense to me now. 

Best, 

Sam.