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SPM  May 2009

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Subject:

Re: Art_Repair, Art_Global

From:

Michael Erb <[log in to unmask]>

Reply-To:

Michael Erb <[log in to unmask]>

Date:

Fri, 15 May 2009 22:20:36 +0200

Content-Type:

text/plain

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text/plain (295 lines)

Ok, it depends on the software version, my version is 'syngo MR B15' and 
you obvious use 'syngo MR 2004A 4VA25A' on a Sonata.

The additional infos are in the Private part of the dicom header,
'Private_0051_1016' means (0051, 1016). This tag should contain a string 
including MOCO, if the data are postprocessed by the online motion 
correction.

The information about the sequence file name is part of 
'Private_0029_1020' (0029, 1020).
If you don't have this tag, I see no chance to find out more details.
You can send an example data file for further analysis to my e-mail.

Michael.

Dorian P. schrieb:
> 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/
>> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>
> 
> 

-- 
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
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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