motion parameter reports for RS data using HCP

[Suss, Stephen]

Hello, 

Forgive the naive question, but I am relative and absolute mean displacements of resting state data as corrected by the HCP pipeline. I am assuming these files below contain this information; however, I was wondering the pipeline generates or is capable of generating, a graphic report. MCFLIRT was indicated in our script: MCType="MCFLIRT."

Movement_AbsoluteRMS_mean.txt

Movement_RelativeRMS_mean.txt

Best,

Steve 

Stephen (Steve) J. Suss Jr., BS

UPMC Research Specialist

Loeffler Building

121 Meyran Avenue

Pittsburgh, PA 15260

[Glasser, Matthew]

No we don’t have a graphic report.  I’ve found computing DVARS after sICA+FIX cleanup to be a good way to identify and quantify motion that strongly influences the image intensities.

Matt.

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[Harms, Michael]

 

Also, the Movement*txt files that don’t end with “mean” contain the actual time series for the run, which you can plot using your preferred plotting tool.

 

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Michael Harms, Ph.D.

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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, Matthew" <glas...@wustl.edu>

Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Friday, November 20, 2020 at 9:23 AM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>

Subject: Re: [hcp-users] motion parameter reports for RS data using HCP

 

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[Stephen Suss]

Okay! Sounds good. Just curious, is there web guide for computing DVARS that includes recommend cut offs? 

Best,

Steve 

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[Glasser, Matthew]

There are publications (e.g. from Jonathan Power) that describe the implementation.  Something like abs(DVARS)-median(DVARS) of 11-15 is good for identifying motion epochs.

Matt.

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[Vadim Axelrod]

Dear Matt,

I found your answer regarding DVARS cut-off values, but it was not clear to me what you meant by "abs(DVARS)-median(DVARS) of 11-15" ?  

Instead of horizontal threshold, abs(DVARS)-median(DVARS) results in a time-course which is far below the DVARS values.

Do you have a reference to Jonathan Power's publication ?

Thank you,

Vadim

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[Glasser, Matt]

You would apply the threshold of 11-15 to that computed timeseries.

 

Matt.

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[Vadim Axelrod]

Thanks, Matt. 

Do you have a reference to cite? I think citing a forum's answer might not be liked by a reviewer... :)

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[Glasser, Matt]

I don’t think we have published the specific evidence for the threshold I suggested.  You can choose to use it or not.

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[Harms, Michael]

Note that “baseline” DVARs is highly influenced by image SNR. 

 

Here’s a paper for a principled scaling of DVARS, if you want to look into using it:

https://www.ncbi.nlm.nih.gov/pubmed/29307608

 

cheers,

-MH

 

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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

 

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[Vadim Axelrod]

Yes, thank you.

The "standard" DVARS calculation is indeed very dataset specific. 

I first tried to apply the Power's 0.005% threshold to HCP, but it did not work for whatever scaling I tried...

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