Lifespan 2.0 HCP-Aging & HCP-Development Release

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Elam, Jennifer

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Feb 26, 2021, 7:59:25 PM2/26/21
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News from the Human Connectome Project (HCP)

February 26, 2021

 

Lifespan 2.0 Release of HCP-Aging & HCP-Development Data 

The Lifespan Human Connectome Project (HCP) consortia for HCP-Aging & HCP-Development and Connectome Coordination Facility (CCF) are thrilled to announce the Lifespan 2.0 Release of imaging and behavioral data on the NIMH Data Archive (NDA)!

Lifespan HCP Release 2.0 includes cross-sectional visit 1 (V1) preprocessed structural and functional imaging data, unprocessed V1 imaging data for all included modalities (structural, high-res hippocampal T2, resting state fMRI, task fMRI, diffusion, and ASL), and non-imaging demographic and behavioral assessment data from 725 HCP-Aging (HCP-A, ages 36-100+) and 652 HCP-Development (HCP-D, ages 5-21) healthy participants, respectively (22+ TB of data/project!). 

What’s new in the Lifespan 2.0 release?

  • Preprocessed rfMRI and tfMRI data available for ALL release subjects
  • Processed sMRI and fMRI data in modality- and processing output-specific "HCP package" datasets 
    • HCP packages cater to different analysis purposes can be used as filters on the Lifespan 2.0 NDA Query page to create custom download packages
    • Most users should access Preprocessed Recommended data that have been cleaned of spatially specific structured noise and precisely aligned across subjects by multimodal cortical surface registration (MSMAll) 
  • Behavioral and biomeasure data available for all released subjects, including NIH Toolbox measures for most subjects. 

Get Access and Download the data: Get started with the Data Access and Download Instructions for navigating NDA and using it's download tools. We've also created a wiki that details setup steps for downloading data via NDA's command line tools.

If you have trouble navigating the NDA for getting access or downloading the data using their tools do not hesitate to contact the NDA helpdesk. NDA needs your user feedback. 

Want more information?  Check out our updated documentation to help with understanding the file structure and interpreting the data:

Join the Community. If you are actively using HCP data and tools, we encourage you to join and be active in the HCP-Users Google group, so that you can ask questions and tune in to technical discussions on issues that may be of interest. Once you have joined (posts from nonmembers are moderated to control spam), post questions to hcp-...@humanconnectome.org.  

Thanks again for your interest in HCP Lifespan and enjoy the data!

Best,

Lifespan consortia for HCP-Aging & HCP-Development and the Connectome Coordination Facility


Yen-Wen Chen

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Sep 13, 2021, 5:44:23 PM9/13/21
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Hello, 

I am wondering if total scores (raw and T scores) of Achenbach Adult Self Report syndromes and DSM-oriented scales are also available in 2.0 Release? 

I downloaded the behavioral data, but only item scores for ASR were included in the downloaded text file.

Any information from you will be very helpful. 

Thank you.

Sincerely, 
Samantha

Elam, Jennifer

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Sep 13, 2021, 10:47:07 PM9/13/21
to Yen-Wen Chen, HCP-Users
Hi Samantha,
The scores for ASR are not included in the 2.0 release. We are planning to include scores for instruments such as ASR in the next Lifespan Release (release date to be determined). In the meantime, if you have access to ASR instruments/scoring sheets at your institution you could calculate the scores from the raw data. 

Best,
Jenn
From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Sent: Monday, September 13, 2021 4:44 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Elam, Jennifer <el...@wustl.edu>; hcp-an...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: Re: Lifespan 2.0 HCP-Aging & HCP-Development Release
 

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Yen-Wen Chen

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Sep 14, 2021, 2:48:18 PM9/14/21
to HCP-Users, el...@wustl.edu, Yen-Wen Chen
Hello Jenn, 

Thank you for the response and the clarification. 

I will ask around if our institute has ASR scoring sheet. 

I have another quick question about the NEO-FFI global five traits total score calculation. 
(1) Does the global total score is the raw total from the respective 12 items? Would the T scores for global five traits be available? 
(2) How was the total score calculated when there are missing data ("NaN") in respective items? From the formula provided in the crosstalk csv ('hcp_choices_calc'), it looks like the missing data is omitted when calculated the total, but the total scores from the downloaded data seems to treat those missing data as 0 (not missing)... 
For example, there is one subject had a missing item for Agreeableness and this subject's Agreeableness total score was calculated with this item treated as "5" (this item is happened to be a reverse item). 

Any information would be very helpful. Thank you so much.

Best, 
Sam. 

yen-we...@stonybrook.edu

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Sep 14, 2021, 3:03:23 PM9/14/21
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My apology. I mistakenly calculated the NEO-FFI global total scores… 

It looks like the total scores from the downloaded data did omit the missing items. My question now is that would it make sense to use the global total score even when there are missing items? 

I apologize for causing the confusion. 

Thank you. 

Best,
Sam. 


Sent from my iPhone

On Sep 14, 2021, at 14:48, Yen-Wen Chen <yen-we...@stonybrook.edu> wrote:

Hello Jenn, 

Jingli_Qu

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Feb 12, 2022, 5:27:27 AM2/12/22
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Hello Jenn,

I was wondering when  preprocessed or processed diffusion data in HCP-D will be released? Any information from you will be helpful!

Looking forward to your reply! Thank you!

Best Wishes!
Qu

Elam, Jennifer

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Feb 14, 2022, 12:03:45 PM2/14/22
to HCP-Users
Hi Qu,
We haven't settled on a release date for the next release that will include preprocessed diffusion data, but it won't be until the late summer of 2022, at the earliest.  We are still figuring out a fix for the diffusion data due to the use of a vitamin E capsule (causes a distortion) at some sites and no capsule at others.

Best,
Jenn 
From: Jingli_Qu <lili...@gmail.com>
Sent: Saturday, February 12, 2022 4:27 AM
Subject: [hcp-users] Re: Lifespan 2.0 HCP-Aging & HCP-Development Release
 

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Hello Jenn,
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Yen-Wen Chen

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Feb 17, 2022, 2:59:09 PM2/17/22
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Hello Jenn,

I am wondering if this scenario (some subjects had the vitamin E capsule, whereas some subjects had not) also applies to HCP-Aging data? We also noticed that some subjects had vitamin E capsule in T1w images but not in T2w and/or functional images, some subjects had vitamin E capsule on all structural and functional scans, while some subjects did not have the capsule on all structural and functional scans.

Thank you.

Best, 
Samantha 

Glasser, Matt

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Feb 17, 2022, 3:12:50 PM2/17/22
to hcp-...@humanconnectome.org, Elam, Jennifer

This isn’t really an issue for external users.  We’ll be providing data that addresses it. 


Matt.

Harms, Michael

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Feb 17, 2022, 3:13:48 PM2/17/22
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Yes, the concern about the fiducial marker applies to the diffusion (dMRI) data of HCP-A as well.  I don’t recall seeing the marker ever showing up well in the gradient echo fMRI scans.  Do you have such an example?

 

-- 

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' via HCP-Users <hcp-...@humanconnectome.org>


Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, February 17, 2022 at 1:59 PM

Harms, Michael

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Feb 17, 2022, 3:15:12 PM2/17/22
to hcp-...@humanconnectome.org, Elam, Jennifer

 

Just to elaborate, it is an issue that external users would need to be concerned about if they are trying to process the ‘unprocessed’ dMRI data from scratch themselves.

 

-- 

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: "Glasser, Matt" <glas...@wustl.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, February 17, 2022 at 2:12 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Cc: "Elam, Jennifer" <el...@wustl.edu>
Subject: Re: [hcp-users] Re: Lifespan 2.0 HCP-Aging & HCP-Development Release

 

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Glasser, Matt

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Feb 17, 2022, 3:16:11 PM2/17/22
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I wouldn’t recommend they do that.


Matt.

Yen-Wen Chen

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Feb 17, 2022, 3:24:44 PM2/17/22
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Hi Matt and Michael, 

Thank you for the quick response and clarification.

Since HCP-Aging has not released preprocessed diffusion data (or has it been released?), we plan to use unprocessed diffusion data.

Do you have suggestions that how we can handle this issue before the processed diffusion is released? 

Thank you.

Best, 
Sam. 

Harms, Michael

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Feb 17, 2022, 3:28:17 PM2/17/22
to hcp-...@humanconnectome.org, Glasser, Matt, Elam, Jennifer

 

I’m sorry, but we are working through the issue ourselves, and we don’t have the bandwidth to provide further guidance and details at this time.

 

-- 

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

 

Yen-Wen Chen

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Feb 17, 2022, 3:29:46 PM2/17/22
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Hi Michael, thank you for the clarification!

Harms, Michael

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Feb 17, 2022, 3:32:02 PM2/17/22
to hcp-...@humanconnectome.org, Glasser, Matt, Elam, Jennifer

 

Actually, there is one piece of simple guidance I can provide, which is that this issue only impacts the data collected at UMN (for HCP-A and HCP-D) and Harvard (HCP-D).

 

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

 

Yen-Wen Chen

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Feb 17, 2022, 3:37:20 PM2/17/22
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Hi Michael, 

Thank you for the information. That's very helpful!

Best, 
Sam. 

Glasser, Matt

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Feb 17, 2022, 3:38:24 PM2/17/22
to hcp-...@humanconnectome.org, Elam, Jennifer

You should wait till we handle it.  The issue is complicated and should only be handled once correctly by folks who know the intricacies of the problem and have the inside information about which scans are affected, etc.  It has taken a while to address the issue precisely because it is complicated and needs to be done carefully to be done well. 

 

Overall, it is not a best practice for folks to be processing the unprocessed HCP data or reprocessing the data for most studies.  Such reprocessing should only be limited to rare methods studies that are trying to improve upon what the HCP did (e.g., to compare a new/better method with standard HCP processing).  Otherwise, you are potentially contributing to reproducibility issues in neuroimaging.  HCP processing has been carefully thought out, drawing from the expertise of a wide variety of field experts and will fit the needs of most studies.  Most individual investigators don’t have this level of multi-modal methods expertise themselves, aren’t particularly interested in the details of the methods and the particulars of the relevant issues (being more interested instead in whatever question they want to use the data for), and will not make as good choices as a result.  I see these kinds of unforced errors again and again in peer review of studies using HCP data. 

Yen-Wen Chen

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Feb 17, 2022, 3:43:22 PM2/17/22
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Hi Matt, 

Thank you for the clarification. We understand that this is an extreme challenge task and we look forward to the processed data to be released! 

Best, 
Sam. 

Yen-Wen Chen

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Jun 27, 2022, 2:13:08 PM6/27/22
to HCP-Users, el...@wustl.edu, Yen-Wen Chen
Hello, 

I have a question about HCP-Aging 2.0 release ASR and OASR data. 

Because the total score (and T-score) had not been released in the 2.0 release, we obtained the ASR/OASR scoring sheets and would like calculate the total scores. 

According to the scoring sheets, the Adult Self-Report (ASR) has 120 items (Scale I - VIII + Other problems) and Older Adult Self-Report (OASR) has 113 items (Scale I - VII + Other problems). However, the 2.0 released asr01.txt file only had 79 ASR ("asr") items and 62 items ("oasr_ppl"). 

Is this because the ASR/OASR data had not been fully released yet in the 2.0 release (only part of the items was released?)? 

PS. I downloaded the behavioral data again today (June 27th 2022) and noticed that there are far more items in the asr01.txt file but many did not have data (no values). 

I would appreciate it if anyone can clarify it.

Thank you.

Best, 
Samantha


On Monday, September 13, 2021 at 10:47:07 PM UTC-4 el...@wustl.edu wrote:

Elam, Jennifer

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Jun 27, 2022, 3:30:15 PM6/27/22
to Yen-Wen Chen, HCP-Users, Lenzini, Petra, Barch, Deanna
Hi Samantha,
We used a shortened form of both ASR and OASR for HCP-Aging and some items were skipped. For this reason, we don't provide total scores and T-scores for these instruments as part of the released data. We also don't recommend comparing HCP-Aging ASR results with that of other studies unless only using data from items asked.  The data is most useful for comparisons of participants within the HCP-Aging study itself.

We have uploaded all ASR/OASR data for visit 1 of the subjects currently released. We will be releasing more data for additional subjects and visit 2 data for longitudinal subjects, but for ASR/OASR the same variables will be used (i.e. no additional items or scoring data will be included).

The extra empty variables/NDA elements that you notice when you download the data are an artifact of NDA's mapping process over several studies. We did not use all NDA elements that NDA has defined for asr01. You can avoid the empty columns by selecting "Exclude null columns" when you create a package for download.
From: Yen-Wen Chen <yen-we...@stonybrook.edu>
Sent: Monday, June 27, 2022 1:13 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Elam, Jennifer <el...@wustl.edu>; Yen-Wen Chen <yen-we...@stonybrook.edu>

Samantha (Yen-Wen) Chen

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Jun 27, 2022, 4:11:04 PM6/27/22
to Elam, Jennifer, HCP-Users, Lenzini, Petra, Barch, Deanna
Hi Jennifer, 

Thank you for your quick response and clarifications. They are very helpful!

I have some follow-up questions. 

(1) If it's the shortened version, can we still calculate item scores into ASR/OASR scales (ASR has 8 scales and one additional scale for Other Problems; OASR has 7 scales and one additional Other Problems)? 

(2) If it's supposed to work like (1), will you suggest using the raw total score for each domain (by using the items that belong to its assigned scale by the original ASR/OASR)?

(3) If it's not supposed to have original ASR/OASR scales in the shortened version, how would you recommend summarizing the item scores? 

Thank you so much.

Best, 
Sam. 
--
Samantha (Yen-Wen) Chen
PhD Candidate of Integrative Neuroscience
Department of Psychology
Stony Brook University
Stony Brook, NY 11790

Elam, Jennifer

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Jun 27, 2022, 4:43:18 PM6/27/22
to Samantha (Yen-Wen) Chen, HCP-Users, Lenzini, Petra, Barch, Deanna, Susan Bookheimer
Hi Sam,
The others on this thread might have more specific advice for you. As long as you do the scoring in a consistent way within the subjects of HCP-Aging you should be able to make comparisons between them. However, I do not have the expertise to give you specific advice on how you should best do this within the context of the ASR scoring sheets for the full ASR.
From: Samantha (Yen-Wen) Chen <yen-we...@stonybrook.edu>
Sent: Monday, June 27, 2022 3:10 PM
To: Elam, Jennifer <el...@wustl.edu>
Cc: HCP-Users <hcp-...@humanconnectome.org>; Lenzini, Petra <plen...@wustl.edu>; Barch, Deanna <dba...@wustl.edu>

Samantha (Yen-Wen) Chen

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Jun 27, 2022, 4:52:06 PM6/27/22
to Elam, Jennifer, HCP-Users, Lenzini, Petra, Barch, Deanna, Susan Bookheimer
Hi Jennifer, 

Thank you for your clarification and suggestion. I will look into ways to score it with the available items. 

This is out of curiosity. How do you decide which items to include/skip? 

In the meantime, I would really appreciate hearing what other people think about this!

Thank you.

Best, 
Sam. 

Barch, Deanna

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Jun 28, 2022, 7:05:59 AM6/28/22
to Elam, Jennifer, Samantha (Yen-Wen) Chen, Susan Bookheimer, Lenzini, Petra, HCP-Users
You will not be able to use the t-scores or compare raw scores for incomplete scales in this sample to others (unless yo average).  However, you can sum the ones within preexisting scales and compare across individuals in this sample.  Deanna Barch
-----------------------------------
Deanna M. Barch, Ph.D.
Professor and Chair, Department of Psychological & Brain Sciences
Gregory B. Couch Professor of Psychiatry
Editor-in-Chief, Biological Psychiatry: Global Open Science
Departments of Psychological & Brain Sciences, Psychiatry, and Radiology
Washington University
Box 1125
One Brookings Drive
St. Louis, MO 63130
Phone:  314-935-8729 or 314-362-2608
Fax: 314-935-8790
Email: dba...@wustl.edu
My Pronouns:  She, her hers

Note:  My work/life balance means that I sometimes work evenings and weekends to free up other times. I do not assume you have the same work/life balance plan, and you should only respond during your own working hours.

Samantha (Yen-Wen) Chen

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Jun 28, 2022, 11:38:51 AM6/28/22
to Barch, Deanna, Elam, Jennifer, Susan Bookheimer, Lenzini, Petra, HCP-Users
Hi Deanna, 

Thank you for your input and suggestions. They are very helpful!

Best, 
Sam.  

Holly Fleischmann

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Nov 12, 2023, 10:23:33 PM11/12/23
to HCP-Users, yen-we...@stonybrook.edu, el...@wustl.edu, Susan Bookheimer, plen...@wustl.edu, HCP-Users, Barch, Deanna
Hi all,
I've read through this thread as I would like to use the ASR data in my study comparing within the HCP-Aging data. I understand why the subscale scores were not given. I'm wondering if anyone has the ASR instruments/scoring sheets in order to calculate the scores from the raw data? I tried to find them online but it looks like the details of which items are scored for each subscale is not available. Any guidance would be great, thank you! 
Best,
Holly

Elam, Jennifer

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Nov 13, 2023, 9:58:46 AM11/13/23
to Holly Fleischmann, HCP-Users, yen-we...@stonybrook.edu, Susan Bookheimer, Lenzini, Petra, Barch, Deanna
Hi Holly,
The ASR is a proprietary instrument that requires labs to pay for the scoring materials that is why you aren't finding them online. Perhaps colleagues at your institution have used ASR and can help you.

Best,
Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org


From: Holly Fleischmann <holly.fl...@gmail.com>
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