Dear All,
You are still best of including realignment parameters (and preferably volterra expansion of the motion parameters). To remove any residual variance due to motion.
To prove this hunch you could do an F-test across the realignment parameters (and preferably volterra expansion of the motion parameters) and look to see what variance is explained by these extra regressors with/without
With regard to extra motion regressors, provided the motion is not highly correlated with your task then you will explain more variance with your model and increase the statistical power of your experiment because you will be looking at the same signal change relative to smaller residual (unexplained) variance.
Reviewers who believe that any scanners can remove all the variance related to motion are individuals who are highly susceptible to marketing I suspect. The reviewer does have one point that the motion you have shown (after PACE and MOCO) is not an accurate reflection of the motion of the subject which is independent of the scanner/sequence details.
David
______________________________________
David Carmichael PhD MInstP
Senior Research Fellow in MR Physics
Department of Clinical and Experimental Epilepsy
UCL Institute of Neurology
Correspondence to:
Advanced Magnetic Resonance Imaging Group
12 Queen Square
London WC1N 3AR
Tel +44 (0)20 76762006
Fax +44 (0)20 76762005
email [log in to unmask]
-----Original
Message-----
From: SPM (Statistical Parametric
Mapping) [mailto:[log in to unmask]] On
Behalf Of jian chen
Sent: 15
May 2009 08:21
To: [log in to unmask]
Subject: Re: [SPM] Art_Repair,
Art_Global
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. < >:
> > 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 >
MSN NZ Travel Find a way to cure that travel bug