about minimally preprocess pipeline

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Ashkan Jafari

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Oct 2, 2021, 5:54:53 AM10/2/21
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Dear Everybody,
I am working on 100 unrelated minimally preprocessed rest-fMRI. I read the HCP manually PDF several times but I just got blurry things and didn't get exactly what minimal preprocess do.
It would be your kindness if you help me and tell me which ones of below preprocesses are included or not in minimal preprocess:
Temporal Filtering
Motion Regression
Voxel normalization
Global Signal Regression
Tissue Regression
 
Wish all of you great moments,
Best Regards,
- Ashkan

Elam, Jennifer

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Oct 4, 2021, 5:27:46 PM10/4/21
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Hi Ashkan,
Please take a look at the Glasser et al. 2013 paper where the preprocessing is discussed. You also might look at the HCP Pipelines Github.

Jenn
From: Ashkan Jafari <ashkan.j...@gmail.com>
Sent: Saturday, October 2, 2021 4:54 AM
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Subject: [hcp-users] about minimally preprocess pipeline
 

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Coalson, Timothy Scott (S&T-Student)

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Oct 4, 2021, 6:00:27 PM10/4/21
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We mainly use ICA FIX to do what motion regression (and part of global signal and tissue regression) are intended to do.  I think most of the released data uses motion-derived regressors in addition to ICA FIX, hopefully someone else knows the specifics.

We don't do temporal filtering (the only "high pass" we did was intended to only serve as a linear detrend, and in newer projects we use an actual linear detrend instead), GSR, or tissue regression.

As for normalization, internally the processing occasionally uses a different normalization and then backs it out afterwards, but I think the main outputs use a grand mean of 10,000 scaling of the cleaned BOLD.

We are also working on separating the neural and non-neural components of the global signal, as a less destructive way to do what GSR is intended to do, but that isn't released yet.

Tim


From: Elam, Jennifer <el...@wustl.edu>
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Glasser, Matt

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Oct 4, 2021, 6:03:00 PM10/4/21
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Movement regression is currently “in” but it will be out with the new denoising.  It is not beneficial above and beyond sICA+FIX.


Matt.

Harms, Michael

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Oct 4, 2021, 6:23:08 PM10/4/21
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FWIW, I believe that the grand mean 10000 scaling is based on the “minimally-preprocessed data” (output of ‘fMRIVolume’), not the FIX-cleaned data.

 

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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

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

 

From: "Coalson, Timothy Scott (S&T-Student)" <tsc...@mst.edu>
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