Hi All,
what about unwarping as a method for "treating" stimulus-correlated
movement effects. I've never tried this method myself, but probably
someone else could comment here?
Best,
Eva
On Fr, 27.08.2010, 09:28, Karsten Specht wrote:
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> Date: Fri, 27 Aug 2010 09:28:57 +0200
> Reply-To: Karsten Specht <[log in to unmask]>
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> From: Karsten Specht <[log in to unmask]>
> Subject: Re: [SPM] realignment parameters effect
> Comments: To: Gandolla Marta <[log in to unmask]>
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> <body class=3D"mceContentBody " style=3D"DISPLAY: block"><span
> style=3D"fon=
> t-size: 9pt;"><span style=3D"font-family: verdana,geneva;"><span
> style=3D"b=
> ackground-color: transparent;"><span style=3D"color: #000000;"><span
> style=
> =3D"color: #000000;">Dear Marta<br /><br />just for emphasising what Chris
> =
> wrote:<br />While many people include the realignment parameter in the
> desi=
> gn matrix, I guess, almost the same number of people don't do that.<br
> />An=
> d, as Chris wrote earlier, including the realignment parameter in case of
> p=
> aradigm correlated movements "kills" your activation, since the
> realignment=
> parameter are capturing all variance and they are in the worst case not
> or=
> thogonal to your paradigm.<br />Having said that, your highest priority
> sho=
> uld be to prevent those paradigm correlated movements since you never can
> b=
> e sure whether you are looking at an activation or a movement artefact.
> And=
> the suggestions that Chris made for preventing movements may be already
> en=
> ough in your case.<br /><br />Good luck<br /><br />Karsten<br /><br
> />--&nb=
> sp;<br />-------------------------------------------------------------<br
> /=
>>Karsten Specht, PhD<br /><br
>> />Department of Biologica=
> l and Medical Psychology<br /><br />Bergen fMRI group<br
> /><=
> br />University of Bergen<br
> />Jonas Lies vei 91<b=
> r />5009 Bergen<br />Norway<br />Tel.: +47-555-86279<br
> />Fax:&nb=
> sp;+47-555-89872<br />[log in to unmask] <br
> />http://fmri.ui=
> b.no/
> <blockquote style=3D"border-left: 2px solid blue; margin-left: 5px;
> padding=
> -left: 5px; padding-top: 5px;">
> <hr />
> <b>Von:</b> Gandolla Marta <[log in to unmask]><br /><b>Ge=
> sendet:</b> 26.aug.2010 20:00:19<br /><b>An:</b> [log in to unmask]<br
> /><b=
>>Betreff:</b> Re: [SPM] realignment parameters effect<br /><br />
> <div>well, sorry for bothering you all again...</div>
> <div>my concern is that quite everyone in literature uses realignment
> param=
> eters as covariats of no interest... do you think it is ok not to use
> them?=
> </div>
> <div>thanks for the help</div>
> <div>marta<br /><br /></div>
> <div class=3D"gmail_quote">2010/8/26 Chris Watson <span><<a href=3D"mail=
> to:[log in to unmask]">[log in to unmask]
> arvard.edu</a>></span><br />
> <blockquote class=3D"gmail_quote" style=3D"border-left: #ccc 1px solid;
> mar=
> gin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Don't include motion
> parameters=
> as regressors.<br /><br />I'm sure you already do this, but I've seen
> that=
> it's good to have a practice session outside of the scanner to see how
> muc=
> h they move when doing the task. Then you can coach them into trying to
> mov=
> e their body less. Also, putting some pillows under their knees, so their
> f=
> eet are elevated, helps quite a bit. And of course vacuum bags, tape
> across=
> the forehead, etc.<br /><br />Gandolla Marta wrote:<br />
> <blockquote class=3D"gmail_quote" style=3D"border-left: #ccc 1px solid;
> mar=
> gin: 0px 0px 0px 0.8ex; padding-left: 1ex;">
> <div class=3D"im">Hi Chris and list,<br /> so, what do you
> sugg=
> est?<br /><br /></div>
> <div>
> <div></div>
> <div class=3D"h5">2010/8/26 Chris Watson <<a target=3D"_blank" href=3D"m=
> ailto:[log in to unmask]">Christopher.Watson@children=
> s.harvard.edu</a> <mailto:<a target=3D"_blank" href=3D"mailto:Christophe=
> [log in to unmask]">[log in to unmask]</a=
>>>><br /><br /> I think that for something as simple as a=
> nkle dorsiflexion, if the<br /> results are in a plausible
> loca=
> tion, you can believe them. The<br /> motion really isn't that
> =
> bad. It's hard to keep a patient still<br /> when doing foot
> mo=
> vements, so there will probably always be<br />
> stimulus-correl=
> ated motion, and if you include the motion<br /> parameters as
> =
> regressors (as you have seen already), it'll get rid<br /> of
> a=
> ny true activation.<br /><br /> Gandolla Marta wrote:<br /><br
> =
> /> Hi Chris and everyone else!!<br />
>  =
> ; indeed, we are looking at right ankle dorsiflexion
> an=
> d yes,<br /> I definitively agree that the
> activa=
> tion seems to be quite<br /> posterior.<br
> />&nbs=
> p; the graph I posted has on x axis the number of scan
> =
> (TR=3D3secs,<br /> 5 minutes of acquisition). on
> =
> the y axis there are mm for<br /> blue, green
> and=
> d line, and degrees for yellow, cyan and<br />
> m=
> agenta line. I superimposed all the realignemnt parameters<br />
> &nbs=
> p; along with the block design to search for the eventual<br
> /=
>> correlation. I attached in any case te SPM
>> outp=
> ut of realignment.<br /><br /> all my best<br
> />&=
> nbsp; marta<br /> 2010/8/26
> C=
> hris Watson<br /> <<a target=3D"_blank" href=
> =3D"mailto:[log in to unmask]">Christopher.Watson@chi=
> ldrens.harvard.edu</a><br /> <mailto:<a target=
> =3D"_blank"
> href=3D"mailto:[log in to unmask]">Christ=
> [log in to unmask]</a>><br /> =
> <mailto:<a target=3D"_blank" href=3D"mailto:Christopher.Watson@childrens=
> .harvard.edu">[log in to unmask]</a><br />
> &nbs=
> p; <mailto:<a target=3D"_blank" href=3D"mailto:Christopher.=
> [log in to unmask]">[log in to unmask]</a>&=
> gt;>><br /><br /><br /> Is it right=
> ankle dorsiflexion that you're looking at?<br />
>  =
> ; It looks pretty posterior to the motor strip; what does it
> look<br=
> /> like overlaid on a structural?<br
> />&=
> nbsp; What's the scale (units) of the graph
> you=
> posted? Can you<br /> post the<br />
>  =
> ; output of SPM's realignment?<br /><br /><br
> /> =
> Gandolla Marta wrote:<br /><br />
> =
> Hi everyone,<br />
> =
> I attached a pdf file instead of
> a=
> docx of the previous<br />
> =
> e-mail. sorry for the inconvenience!!<br />
> &nb=
> sp; I'd need some help about realignment
> paramet=
> ers<br /> effect that<br />
> &=
> nbsp; seems to be huge in the acquisition I will now
> d=
> escribe.<br /> We have a
> 30=
> secs block design, starting from rest. The<br />
>  =
> ; patient is performing active ankle dorsiflexion
> duri=
> ng<br /> on blocks.<br />
> &nb=
> sp; We did the following preprocessing steps:<br
> />&nb=
> sp; - realignment<br />
> &nb=
> sp; - coreg<br />
> &n=
> bsp; - normalize<br />
> &nbs=
> p; - smooth (6mm)<br />
> &nb=
> sp; then we implemented the GLM with a 8 columns design
> matrix=
> <br /> (1-condition with
> th=
> e 30 secs block design, 2-7- realign<br />
>  =
> ; param, 8- baseline) and we found zero activation<br
> /> =
> ; (p<0.01 FWE<br />  =
> ; corrected).<br />
> =
> we then chacked with the 2 columns design matrix<br />
> =
> (1-condition<br />
> &n=
> bsp; with the 30 secs block design, 2- baseline) and we found a<br
> /> =
> quite important activation
> (fig.=
> 1). should we trust this<br />
> &nb=
> sp; activation? the realignemnt param plot along with the block<br
> /> =
> design protocol is shown in
> fig.=
> 2. is it possible that all<br />
> &=
> nbsp; this effect depends on the correlation between the<br />
> =
> realignment<br />
> &n=
> bsp; parameters and the condition column in the design matrix?<br />
> =
> should trust only the design
> with=
> the realignement<br /> parameters<br />
> &n=
> bsp; as covariats of no interest? we
> are=
> thinking in this<br /> case why<br />
> &nbs=
> p; we don't see any activation... do we
> =
> miss something?<br />
>  =
> ;thanks for your help<br />
> =
> best regards<br />
> marta<b=
> r /><br /><br /><br /></div>
> </div>
> </blockquote>
> </blockquote>
> </div>
> <br /></blockquote>
> </span></span></span></span></span></body>
> --002215048f637250f9048ebdc501--
>
>
--
Mag. Dr. Eva-Maria Seidel
Research Associate
Department of Clinical, Biological, and Differential Psychology
Faculty of Psychology, University of Vienna
http://psychologie.univie.ac.at/klinische-psychologie
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