Dear Michael,
There is no ImageComments field and Matlab stops already at the first 'if':
??? Reference to non-existent field 'Private_0051_1016'.
The second part produces empty 'id' variable. I am searching for
headers related but cannot find any. I paste some of them so maybe can
help to understand:
(0008, 1090) ModelName LO 6 Sonata
(0018, 0020) ScanningSequence CS 6 SE\EP
(0018, 0021) SequenceVariant CS 2 SK
(0018, 0022) ScanOptions CS 2 FS
(0018, 0023) MrAcquisitionType CS 2 2D
(0018, 0024) SequenceName SH 12 *epfid2d1_64
(0018, 0083) NumberOfAverages DS 2 1
(0018, 1020) SoftwareVersion LO 22
syngo MR 2004A 4VA25A
(0020, 0032) ImagePositionPatient DS 50
-655.23438544808\-675.3511048114\-43.520873569747
(0020, 0037) ImageOrientationPatient DS 102
0.99438639119084\0.00982883234734\0.10535226181312\5.305355311e-008\0.99567618628965\-0.0928920451691
(0020, 0052) FrameOfReferenceUid UI 50
1.3.12.2.1107.5.2.12.21909.20081116131646781.0.0.0
(0020, 1040) PositionReference LO 0
My TR is 2s.
Sorry, but didn't understand how should be done the analysis if the
volumes have a software or hardware correction before I get them on a
CD. Somebody suggested to use the motion parameters from the scanner.
Is this only for software corrected data or also for hardware PACE?
Thank you.
Dorian.
2009/5/15 Michael Erb <[log in to unmask]>:
> 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/
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>
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