realignment may be related to the sequence used as some vendors offer an
optional onlein motion correction. The issue then is that motion has
already (partly) been corrected online during the scan. Some people do
not like to use it as only the second-to-last scan is used to correct
the gradient position for the next scan and as the parameters are not
necessarily written out (they may be in your case, Rachel?). Also, if
you would like to use unwarping, this may cause trouble as the
assumptions of the unwarping are not met.
The problem with including SPM's motion parameters is that they also do
not reflect the true motion in the scanner as some of it has already
been accounted for. I therefore tend to agree with the reviewer that
such an approach (using online MoCo but then include SPM's parameters in
the model) is potentially problematic. Not necessarily, and perhaps not
even substantially, but potentially. Just my 2 Euro-cents :)
Dorian P. schrieb:
> Hi all,
> 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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Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
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