Hi Dorian,
on the Siemens scanners there are two methods for motion correction
aviable for epi BOLD one is the software postprocessing as realignment
in SPM and the second is hardware correction by changing slice position
of volume n based on the realignment parameters of volume n-2
(Prospective Acquisition Correction [PACE] ), as described by Peter and
Marko. As far as I know the parameters of the last volume are used if
you include a long enough gap between the volumes (delay in TR).
To find the dicom informations you can do:
hdr=spm_dicom_headers(spm_select); % select your dicom files
if ~isempty(strfind(hdr{1}.Private_0051_1016,'MOCO'))
fprintf('Data are motion corrected!\n');
for p=1:length(hdr)
disp(hdr{p}.ImageComments) % displays motion parameter
end
end
To check if your sequence was ep2d_pace you can do:
id=strmatch('MrPhoenixProtocol',cellstr(char(hdr{1}.CSASeriesHeaderInfo.name)));
if ~isempty(id)
ahead=hdr{1}.CSASeriesHeaderInfo(id).item(1).val;
pos=strfind(ahead,'tSequenceFileName');
[T,R]=strtok(ahead(pos:end),char(10));
[T,R]=strtok(T);
[T,R]=strtok(R); % =
[T,R]=strtok(R); % value
fprintf('Sequence File Name: %s\n', T);
end
> And finally, the idea is realigment can be used in preprocessing but
> not motion parameters in analysis? Then what do we realign for?
This are different things:
first you try to bring together your images as good as possible (realign)
then you may remove residual intensity variations caused by movement
using motion parameters in analysis (regressor of no interest)
As this residual intensity variations depends on the original
measurement process, you cannot use the parameters from the realignment
of pre-corrected data in your model.
Michael.
Dorian P. schrieb:
> 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 >
>
>
--
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Dr. Michael Erb
Sektion f. experimentelle Kernspinresonanz des ZNS
Abteilung Neuroradiologie, Universitaetsklinikum
Hoppe-Seyler_Str. 3, D-72076 Tuebingen
Tel.: +49(0)7071/2987753 priv. +49(0)7071/61559
Fax.: +49(0)7071/294371
e-mail: <[log in to unmask]>
www: http://www.medizin.uni-tuebingen.de/nrad/sektion/
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
