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From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of David V. Smith
Sent: Thursday, May 22, 2014 12:44 PM
To: [log in to unmask]
Subject: Re: [FSL] fsl_motion_outliers question.

 

Hi Michael,

 

Thanks for the explanation here. I have a related followup question regarding "scrubbing" vs including the output of fsl_motion_outliers as a set of confound EVs in my analysis. Would there be any advantage of "scrubbing" (i.e., physically removing or masking) those outlier time points instead of having regressors (i.e., the output of fsl_motion_outliers) to account for them? I think the fsl_motion_outliers documentation still recommends the regression approach over the "scrubbing" approach, but I still see reviewers claiming that outlier time points can only be removed via scrubbing (and not via regression).

 

Thanks,

David

 

 

On May 22, 2014, at 10:04 AM, Harms, Michael wrote:



 

Hi,

I believe that using the confound matrix from fsl_motion_outliers in fsl_regfilt would return a "residualized" time series, with the "mean" added back in, so that the "scrubbed/censored" time points as coded in the confound matrix are replaced by the "mean" of the time series (i.e., their residual is 0).  I put "mean" in quotation marks, because I'm not sure what exactly is added back in -- whether it is the mean of the full time series, which would include the contribution of the time points that you actually want to ignore, or if what is added back in is actually the intercept of the GLM fit (i.e., the mean excluding the time points that you want to ignore).

 

The question becomes what do you intend to do with this output.  For example, you can't just go and do a seed-based correlation analysis with it.  That is not "scrubbing", because you would be pretending that the time points as identified by fsl_motion_outliers are now somehow fully legitimate time points, which isn't the case (i.e., they would contribute to the calculation of the correlation, whereas in the Power et al. approach to scrubbing, the bad time points are masked out the analysis altogether).

 

cheers,

-MH

 

-- 

Michael Harms, Ph.D.

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Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

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

St. Louis, MO  63110  Email: [log in to unmask]

 

From: Andreas Lidström <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, May 22, 2014 5:10 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] fsl_motion_outliers question.

 

I'm no expert, but I would say no. the output is not a time series but a matrix with one column of zeroes for each outlier image, with the affected image being marked by a one, to be included in the 1:st level GLM.

 

2014-05-21 19:54 GMT+02:00 Broulidakis M.J. <[log in to unmask]>:

Dear FSL experts.

 

I haven’t found much information on it online. But is it possible to perform motion scrubbing using the output of fsl_motion_outliers with the command fsl_regfilt? I would be grateful for any advice (even if it is just a yes or no).

 

Best wishes,

 

John

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John Broulidakis

Developmental Brain-Behaviour Laboratory

University of Southampton

 

 

 

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David V. Smith, Ph.D.
Postdoctoral Fellow, Delgado Lab

Department of Psychology

Rutgers University

Newark, NJ 07102

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