HCP-Aging FEAT tfMRI level 2 analysis and Contrasts

[Hye Min Shin]

Hello,

I understand that HCP-YA has FEAT tfMRI level 2 analysis maps and Contrasts.txt files included in preprocessed data. I was going through HCP-Aging data and I realized that FEAT level 2 maps and Contrasts.txt files are not yet included. 

Are there alternate files for FEAT maps and Contrasts.txt files for HCP-Aging data? Also, is the directory fMRI_CONCAT_ALL concatenated across time-series? 

I apologize if these questions are already answered in other documents. However, I looked at both Lifespan HCP 2.0 Reference-Manual -Appendix 1 and NDA HCP-Aging page for reference but to no avail. 

Thank you.

Best,

Julia Shin

[Harms, Michael]

 

We haven’t run task-analysis on the HCP Lifespan studies yet.

 

Yes, fMRI_CONCAT_ALL is across all fMRI runs.  There should be a README file in the directory somewhere that lists the runs included.

 

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: Hye Min Shin <shin...@bu.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Thursday, April 29, 2021 at 10:19 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] HCP-Aging FEAT tfMRI level 2 analysis and Contrasts

 

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[Hye Min Shin]

Thank you for the quick response Professor Harms.

Unfortunately, I tried looking through all the subdirectories in a sample subject's folder released by HCP-Aging. Is it under fmriresults01/HCA*_V1_MR/MNINonLinear/Results folder? There seems to be only 1 readme file and that does not list which runs are included. 

Also, would it be possible to know approximately when task analysis on HCP-Aging data would be released? I wanted to run some preliminary level 2 feat analysis but it would be difficult without the proper design fsf files and Contrasts. 

Best,

Julia Shin

[Glasser, Matthew]

I believe it is under:

 

${StudyFolder]/${Subject}/MNINonLinear/Results /fMRI_CONCAT_ALL

 

Matt.

To view this discussion on the web visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/6157f9bb-d7b9-466d-9703-34d1b4135c29n%40humanconnectome.org.

[Harms, Michael]

 

If you have the “Recommended Functional” package, there should be a

MNINonLinear/Results/<fMRIName>/<fMRIName>_Atlas_MSMAll_<hp>_clean.README.txt

file for each individual run, which lists the runs that went into multi-run FIX.

 

If you have the “Extended Functional” package, there should be a

MNINonLinear/Results/<fMRIConcat>/<fMRI_Concat>_Runs.csv

file that lists the runs, and their starting/stopping frames within the concatenated .dtseries.nii.

 

Sorry, but I’m not going to speculate on when the task-analysis pipeline outputs will be ready for release at this particular point in time.

 

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