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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