If the motion parameters are useless, then also realigment is useless.
I would be curious to hear that reviewer on the topic. How much did
your subjects move in that experiment Mitchell?
This is the first time I read that realigment is related to machine
type. What can be the logic behind that strange reuqest of this
2009/5/14 MITCHELL R.L.C. <[log in to unmask]>:
> On the subject of movement confounds, a reviewer once insisted that I remove the realignment motion parameters from my model.
> He/she stated that since I had scanned with a Siemens machine, and taken advantage of the machine's inbuilt/online prospective and retrospective motion correction, that the mp figures were useless.
> What do people think about this?
> Does anyone agree or disagree?
> Best regards
> Dr. Rachel L. C. Mitchell,
> Lecturer in Psychology, Durham University.
> Honorary Senior Research Fellow, Institute of Psychiatry, KCL.
> Governor, Tees Esk and Wear Valleys NHS Foundation Trust.
> Correspondence Address:
> Dept. of Psychology,
> Durham University,
> Science Site,
> South Road,
> Co. Durham.
> DH1 3LE.
> Phone +44 (0)191 334 3272
> Fax +44 (0)191 334 3241
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Paul Mazaika
> Sent: 13 May 2009 18:57
> To: [log in to unmask]
> Subject: Re: [SPM] Art_Repair, Art_Global
> The art_global function tries to automatically detect bad image volumes according
> to the criteria of unusual global signal, or large scan-to-scan motion,
> or large total motion from baseline. Use it after realignment, because
> it uses the rp.txt file. When used just before estimation, it is
> easier to compare estimation results with and without it, to see if
> it helps on a particular data set.
> The clip function marks a volume for repair if the total motion from
> baseline is > 3mm, which may be useful for short duration artifacts when
> no motion regressors are used in the design matrix.
> Handling artifacts is tricky, and the best method may not yet be known.
> Consequently, the admittedly limited "manual" on the website does not give
> strong guidance on the best choices of parameters.
> Note there are alternative (and better documented!) approaches to the artifact
> problem, including removing volumes by inspection (Luo and Nichols, 2003)
> or by the art_detect utility (Whitfield-Gabrieli), adding scan null regressors
> (Lemieux, 2007), and adaptive weighting of the scans (RobustWLS toolbox).
> Also, motion regressors (e.g. Lund, 2005) are helpful for removing
> the effect of many artifacts.
> ----- Original Message -----
> From: "Sanne Boesveldt" <[log in to unmask]>
> To: [log in to unmask]
> Sent: Wednesday, May 13, 2009 7:15:12 AM GMT -08:00 US/Canada Pacific
> Subject: [SPM] Art_Repair, Art_Global
> Dear all
> I am trying to use art_repair/art_global in SPM5, but what exactly does
> Art-global do? And when do I use it, after realignment, or after
> normalization and smoothing? And what is the function of the 'clip' button
> in the program?
> The only manual I could find are the short .txt and .pdf files from
> http://cibsr.stanford.edu/tools/ArtRepair/ArtRepair.htm, but those don't
> give that much info unfortunately. Is there a better manual out there?
> Sanne Boesveldt, PhD
> Postdoctoral Fellow
> Monell Chemical Senses Center
> 3500 Market Street
> Philadelphia, PA 19104
> +1 267 519 4688
> [log in to unmask]
> Paul K. Mazaika, PhD.
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> Office: (650)724-6646 Cell: (650)799-8319
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