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 > _________________________________________________________________ Find a way to cure that travel bug MSN NZ Travel http://travel.msn.co.nz/