Hi All,

I have a slight different question. If you resliced all your images at realignment stage, would you include the rp*.txt in the model design as regressors? If you do include, dose this mean you include the motion factors twice in the analysis?

Thanks.

Jian

> Date: Thu, 14 May 2009 11:35:09 +0200
> From: [log in to unmask]
> Subject: Re: [SPM] Art_Repair, Art_Global
> To: [log in to unmask]
>
> Hi again,
>
> Is there a DICOM flag to show if the scanner is performing this online
> correction or all Siemens scanners does it?
>
> And finally, the idea is realigment can be used in preprocessing but
> not motion parameters in analysis? Then what do we realign for?
>
> Thank you all.
> Dorian
>
> 2009/5/14 Peter Erhard <[log in to unmask]>:
> > I guess the reviewer believes that the prospective motion correction
> > - that is built into the Siemens EPI sequence -
> > fully removes head motion and related spin history effects.
> > This is not the case, because the motion correction always
> > works on the n+1 volume, hence too late to fully remove head motion
> > (but it removes some of the slower 'drifts' of the head)
> > and it does not correct
> > for spin history effects associated with movement perpendicular to the
> > slice plane.
> > Just my 2 ct.
> > pe
> >
> > On Thu, 14 May 2009, Dorian P. wrote:
> >
> > PE > Hi all,
> > PE >
> > PE > If the motion parameters are useless, then also realigment is useless.
> > PE > I would be curious to hear that reviewer on the topic. How much did
> > PE > your subjects move in that experiment Mitchell?
> > PE >
> > PE > This is the first time I read that realigment is related to machine
> > PE > type. What can be the logic behind that strange reuqest of this
> > PE > reviewer?
> > PE >
> > PE > Dorian
> > PE >
> > PE > 2009/5/14 MITCHELL R.L.C. <[log in to unmask]>:
> > PE > > Hello
> > PE > >
> > PE > > On the subject of movement confounds, a reviewer once insisted that I remove the realignment motion parameters from my model.
> > PE > > 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.
> > PE > >
> > PE > > What do people think about this?
> > PE > > Does anyone agree or disagree?
> > PE > >
> > PE > > Best regards
> > PE > > Rachel
> > PE > >
> > PE > > *************************************************************
> > PE > >
> > PE > > Dr. Rachel L. C. Mitchell,
> > PE > > Lecturer in Psychology, Durham University.
> > PE > > Honorary Senior Research Fellow, Institute of Psychiatry, KCL.
> > PE > > Governor, Tees Esk and Wear Valleys NHS Foundation Trust.
> > PE > >
> > PE > > Correspondence Address:
> > PE > > Dept. of Psychology,
> > PE > > Durham University,
> > PE > > Science Site,
> > PE > > South Road,
> > PE > > Durham,
> > PE > > Co. Durham.
> > PE > > DH1 3LE.
> > PE > > U.K.
> > PE > >
> > PE > > Phone +44 (0)191 334 3272
> > PE > > Fax +44 (0)191 334 3241
> > PE > >
> > PE > >
> > PE > > -----Original Message-----
> > PE > > From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Paul Mazaika
> > PE > > Sent: 13 May 2009 18:57
> > PE > > To: [log in to unmask]
> > PE > > Subject: Re: [SPM] Art_Repair, Art_Global
> > PE > >
> > PE > > The art_global function tries to automatically detect bad image volumes according
> > PE > > to the criteria of unusual global signal, or large scan-to-scan motion,
> > PE > > or large total motion from baseline. Use it after realignment, because
> > PE > > it uses the rp.txt file. When used just before estimation, it is
> > PE > > easier to compare estimation results with and without it, to see if
> > PE > > it helps on a particular data set.
> > PE > >
> > PE > > The clip function marks a volume for repair if the total motion from
> > PE > > baseline is > 3mm, which may be useful for short duration artifacts when
> > PE > > no motion regressors are used in the design matrix.
> > PE > >
> > PE > > Handling artifacts is tricky, and the best method may not yet be known.
> > PE > > Consequently, the admittedly limited "manual" on the website does not give
> > PE > > strong guidance on the best choices of parameters.
> > PE > >
> > PE > > Note there are alternative (and better documented!) approaches to the artifact
> > PE > > problem, including removing volumes by inspection (Luo and Nichols, 2003)
> > PE > > or by the art_detect utility (Whitfield-Gabrieli), adding scan null regressors
> > PE > > (Lemieux, 2007), and adaptive weighting of the scans (RobustWLS toolbox).
> > PE > > Also, motion regressors (e.g. Lund, 2005) are helpful for removing
> > PE > > the effect of many artifacts.
> > PE > >
> > PE > >  -Paul
> > PE > >
> > PE > >
> > PE > >
> > PE > > ----- Original Message -----
> > PE > > From: "Sanne Boesveldt" <[log in to unmask]>
> > PE > > To: [log in to unmask]
> > PE > > Sent: Wednesday, May 13, 2009 7:15:12 AM GMT -08:00 US/Canada Pacific
> > PE > > Subject: [SPM] Art_Repair, Art_Global
> > PE > >
> > PE > > Dear all
> > PE > >
> > PE > > I am trying to use art_repair/art_global in SPM5, but what exactly does
> > PE > > Art-global do? And when do I use it, after realignment, or after
> > PE > > normalization and smoothing? And what is the function of the 'clip' button
> > PE > > in the program?
> > PE > >
> > PE > > The only manual I could find are the short .txt and .pdf files from
> > PE > > http://cibsr.stanford.edu/tools/ArtRepair/ArtRepair.htm, but those don't
> > PE > > give that much info unfortunately. Is there a better manual out there?
> > PE > >
> > PE > > Thanks!
> > PE > >
> > PE > > Sanne Boesveldt, PhD
> > PE > > Postdoctoral Fellow
> > PE > > Monell Chemical Senses Center
> > PE > > 3500 Market Street
> > PE > > Philadelphia, PA 19104
> > PE > > USA
> > PE > >
> > PE > > +1 267 519 4688
> > PE > > [log in to unmask]
> > PE > >
> > PE > > --
> > PE > > Paul K. Mazaika, PhD.
> > PE > > Center for Interdisciplinary Brain Sciences Research
> > PE > > Stanford University School of Medicine
> > PE > > Office:  (650)724-6646             Cell:  (650)799-8319
> > PE > >
> > PE > > CONFIDENTIALITY NOTICE: Information contained in this message and any
> > PE > > attachments is intended only for the addressee(s). If you believe
> > PE > > that you have received this message in error, please notify the
> > PE > > sender immediately by return electronic mail, and please delete it
> > PE > > without further review, disclosure, or copying.
> > PE > >
> > PE >

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